toil 9.1.2__py3-none-any.whl → 9.2.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- toil/__init__.py +5 -9
- toil/batchSystems/abstractBatchSystem.py +23 -22
- toil/batchSystems/abstractGridEngineBatchSystem.py +17 -12
- toil/batchSystems/awsBatch.py +8 -8
- toil/batchSystems/cleanup_support.py +4 -4
- toil/batchSystems/contained_executor.py +3 -3
- toil/batchSystems/gridengine.py +3 -4
- toil/batchSystems/htcondor.py +5 -5
- toil/batchSystems/kubernetes.py +65 -63
- toil/batchSystems/local_support.py +2 -3
- toil/batchSystems/lsf.py +6 -7
- toil/batchSystems/mesos/batchSystem.py +11 -7
- toil/batchSystems/mesos/test/__init__.py +1 -2
- toil/batchSystems/options.py +9 -10
- toil/batchSystems/registry.py +3 -7
- toil/batchSystems/singleMachine.py +8 -11
- toil/batchSystems/slurm.py +49 -38
- toil/batchSystems/torque.py +3 -4
- toil/bus.py +36 -34
- toil/common.py +129 -89
- toil/cwl/cwltoil.py +857 -729
- toil/cwl/utils.py +44 -35
- toil/fileStores/__init__.py +3 -1
- toil/fileStores/abstractFileStore.py +28 -30
- toil/fileStores/cachingFileStore.py +8 -8
- toil/fileStores/nonCachingFileStore.py +10 -21
- toil/job.py +159 -158
- toil/jobStores/abstractJobStore.py +68 -69
- toil/jobStores/aws/jobStore.py +249 -213
- toil/jobStores/aws/utils.py +13 -24
- toil/jobStores/fileJobStore.py +28 -22
- toil/jobStores/googleJobStore.py +21 -17
- toil/jobStores/utils.py +3 -7
- toil/leader.py +14 -14
- toil/lib/accelerators.py +6 -4
- toil/lib/aws/__init__.py +9 -10
- toil/lib/aws/ami.py +33 -19
- toil/lib/aws/iam.py +6 -6
- toil/lib/aws/s3.py +259 -157
- toil/lib/aws/session.py +76 -76
- toil/lib/aws/utils.py +51 -43
- toil/lib/checksum.py +19 -15
- toil/lib/compatibility.py +3 -2
- toil/lib/conversions.py +45 -18
- toil/lib/directory.py +29 -26
- toil/lib/docker.py +93 -99
- toil/lib/dockstore.py +77 -50
- toil/lib/ec2.py +39 -38
- toil/lib/ec2nodes.py +11 -4
- toil/lib/exceptions.py +8 -5
- toil/lib/ftp_utils.py +9 -14
- toil/lib/generatedEC2Lists.py +161 -20
- toil/lib/history.py +141 -97
- toil/lib/history_submission.py +163 -72
- toil/lib/io.py +27 -17
- toil/lib/memoize.py +2 -1
- toil/lib/misc.py +15 -11
- toil/lib/pipes.py +40 -25
- toil/lib/plugins.py +12 -8
- toil/lib/resources.py +1 -0
- toil/lib/retry.py +32 -38
- toil/lib/threading.py +12 -12
- toil/lib/throttle.py +1 -2
- toil/lib/trs.py +113 -51
- toil/lib/url.py +14 -23
- toil/lib/web.py +7 -2
- toil/options/common.py +18 -15
- toil/options/cwl.py +2 -2
- toil/options/runner.py +9 -5
- toil/options/wdl.py +1 -3
- toil/provisioners/__init__.py +9 -9
- toil/provisioners/abstractProvisioner.py +22 -20
- toil/provisioners/aws/__init__.py +20 -14
- toil/provisioners/aws/awsProvisioner.py +10 -8
- toil/provisioners/clusterScaler.py +19 -18
- toil/provisioners/gceProvisioner.py +2 -3
- toil/provisioners/node.py +11 -13
- toil/realtimeLogger.py +4 -4
- toil/resource.py +5 -5
- toil/server/app.py +2 -2
- toil/server/cli/wes_cwl_runner.py +11 -11
- toil/server/utils.py +18 -21
- toil/server/wes/abstract_backend.py +9 -8
- toil/server/wes/amazon_wes_utils.py +3 -3
- toil/server/wes/tasks.py +3 -5
- toil/server/wes/toil_backend.py +17 -21
- toil/server/wsgi_app.py +3 -3
- toil/serviceManager.py +3 -4
- toil/statsAndLogging.py +12 -13
- toil/test/__init__.py +33 -24
- toil/test/batchSystems/batchSystemTest.py +12 -11
- toil/test/batchSystems/batch_system_plugin_test.py +3 -5
- toil/test/batchSystems/test_slurm.py +38 -24
- toil/test/cwl/conftest.py +5 -6
- toil/test/cwl/cwlTest.py +194 -78
- toil/test/cwl/download_file_uri.json +6 -0
- toil/test/cwl/download_file_uri_no_hostname.json +6 -0
- toil/test/docs/scripts/tutorial_staging.py +1 -0
- toil/test/jobStores/jobStoreTest.py +9 -7
- toil/test/lib/aws/test_iam.py +1 -3
- toil/test/lib/aws/test_s3.py +1 -1
- toil/test/lib/dockerTest.py +9 -9
- toil/test/lib/test_ec2.py +12 -11
- toil/test/lib/test_history.py +4 -4
- toil/test/lib/test_trs.py +16 -14
- toil/test/lib/test_url.py +7 -6
- toil/test/lib/url_plugin_test.py +12 -18
- toil/test/provisioners/aws/awsProvisionerTest.py +10 -8
- toil/test/provisioners/clusterScalerTest.py +2 -5
- toil/test/provisioners/clusterTest.py +1 -3
- toil/test/server/serverTest.py +13 -4
- toil/test/sort/restart_sort.py +2 -6
- toil/test/sort/sort.py +3 -8
- toil/test/src/deferredFunctionTest.py +7 -7
- toil/test/src/environmentTest.py +1 -2
- toil/test/src/fileStoreTest.py +5 -5
- toil/test/src/importExportFileTest.py +5 -6
- toil/test/src/jobServiceTest.py +22 -14
- toil/test/src/jobTest.py +121 -25
- toil/test/src/miscTests.py +5 -7
- toil/test/src/promisedRequirementTest.py +8 -7
- toil/test/src/regularLogTest.py +2 -3
- toil/test/src/resourceTest.py +5 -8
- toil/test/src/restartDAGTest.py +5 -6
- toil/test/src/resumabilityTest.py +2 -2
- toil/test/src/retainTempDirTest.py +3 -3
- toil/test/src/systemTest.py +3 -3
- toil/test/src/threadingTest.py +1 -1
- toil/test/src/workerTest.py +1 -2
- toil/test/utils/toilDebugTest.py +6 -4
- toil/test/utils/toilKillTest.py +1 -1
- toil/test/utils/utilsTest.py +15 -14
- toil/test/wdl/wdltoil_test.py +247 -124
- toil/test/wdl/wdltoil_test_kubernetes.py +2 -2
- toil/toilState.py +2 -3
- toil/utils/toilDebugFile.py +3 -8
- toil/utils/toilDebugJob.py +1 -2
- toil/utils/toilLaunchCluster.py +1 -2
- toil/utils/toilSshCluster.py +2 -0
- toil/utils/toilStats.py +19 -24
- toil/utils/toilStatus.py +11 -14
- toil/version.py +10 -10
- toil/wdl/wdltoil.py +313 -209
- toil/worker.py +18 -12
- {toil-9.1.2.dist-info → toil-9.2.0.dist-info}/METADATA +11 -14
- {toil-9.1.2.dist-info → toil-9.2.0.dist-info}/RECORD +150 -153
- {toil-9.1.2.dist-info → toil-9.2.0.dist-info}/WHEEL +1 -1
- toil/test/cwl/staging_cat.cwl +0 -27
- toil/test/cwl/staging_make_file.cwl +0 -25
- toil/test/cwl/staging_workflow.cwl +0 -43
- toil/test/cwl/zero_default.cwl +0 -61
- toil/test/utils/ABCWorkflowDebug/ABC.txt +0 -1
- {toil-9.1.2.dist-info → toil-9.2.0.dist-info}/entry_points.txt +0 -0
- {toil-9.1.2.dist-info → toil-9.2.0.dist-info}/licenses/LICENSE +0 -0
- {toil-9.1.2.dist-info → toil-9.2.0.dist-info}/top_level.txt +0 -0
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toil/test/wdl/wdltoil_test.py,sha256=fqqJD2K1zoJMdUkgetAKFtV9qSDrfMQ-bZrTcFpcnGM,57615
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321
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toil/test/wdl/wdltoil_test_kubernetes.py,sha256=AEyWxMNtmS9-TBMwyCumHYQQ0DLHQp6T8StpRSxsnR8,2996
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toil/test/wdl/md5sum/empty_file.json,sha256=Y4Yb2dygeV8J7wowyUuTi8qOwmRR-znb70r3jsPw688,27
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toil/test/wdl/md5sum/md5sum-gs.json,sha256=PppK5H77nRcpo_n2ttZzEPkoxrLVypGlFD6Wrwe-hfk,123
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toil/test/wdl/md5sum/md5sum.1.0.wdl,sha256=BJMdlruHIRcuBLQY738T_eyHZms-8obz4-P6VxrwW30,445
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@@ -429,24 +426,24 @@ toil/test/wdl/wdl_specification/v1_spec_declaration.wdl,sha256=-9YcGU3YotQP3vn4-
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toil/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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toil/utils/toilClean.py,sha256=X6Fws6LVqa-ScUITMTomV5iohXa3yz_rAIFnUfXlqZU,1850
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toil/utils/toilConfig.py,sha256=Ki6gGV-9d21z06u-A0meE2H0MjJUCT4mQEsMmERHn8o,1502
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toil/utils/toilDebugFile.py,sha256=
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toil/utils/toilDebugJob.py,sha256=
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toil/utils/toilDebugFile.py,sha256=t-WVOca8Imluf_xf6FA5TTE2NXWEkbjXCSkJorBAb2s,6260
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430
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toil/utils/toilDebugJob.py,sha256=AtCTmkZyh9Rayvo0lH9BcOUEL9xyMrCe5q-NOP-eei0,10765
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toil/utils/toilDestroyCluster.py,sha256=OvwlKgomHiLptN8GjLouBzfFCo-SyLfrRWF4sv0kPww,1416
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toil/utils/toilKill.py,sha256=21zOstvFb32cwQlhMsG5Q4lPT2CSnZ7OXEK1mmyLmtk,2751
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-
toil/utils/toilLaunchCluster.py,sha256=
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toil/utils/toilLaunchCluster.py,sha256=bFwgJ40tY0vKjUvqAC8_QxSPJXz80DpUr3FgzN1DRMU,12900
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toil/utils/toilMain.py,sha256=Lz7dtkpE8urTRgimRjewKvbh4Xgh6l0OJRtxX203LyI,2790
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toil/utils/toilRsyncCluster.py,sha256=cR-4o9KpoyBdObCwQgpAqpO30VK3gGzwHKOGyQHGQeQ,2150
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toil/utils/toilServer.py,sha256=4XbyOHQHgMWWrCWj9Uz1M-jLQheV2Ju-DQ_fNdnBg1o,1178
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toil/utils/toilSshCluster.py,sha256=
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toil/utils/toilStatus.py,sha256=
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toil/utils/toilSshCluster.py,sha256=VrMprvZf2AfTvWAoa0v_t_81T1Q6Nf1cdzEjJV-r-UE,3582
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toil/utils/toilStats.py,sha256=P2OEdDcsTjZzVqgD_Wq4-OgBQDNIBBeI3p6Br0_Ktws,26124
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toil/utils/toilStatus.py,sha256=Mxpbd5vx0Ff-LvRmd0SHD2tCIH9ZJiuUQksUGT0P9T4,20361
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toil/utils/toilUpdateEC2Instances.py,sha256=47972f1_oRvKOZv77EcBr3QjP2YNl8SZWhTsw6mWG-4,1318
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toil/wdl/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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toil/wdl/utils.py,sha256=U0TqbVTsap0VdeZjrUf4l71A7Zns-Hkso1B1Zdp2LRk,1316
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+
toil-9.2.0.dist-info/licenses/LICENSE,sha256=YVxVi652J1ZDmtC3EMP5r0EbK85-hm_pzogiULmlqUA,12862
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toil-9.2.0.dist-info/METADATA,sha256=Dbp0s2tHZNz3aTDgW5p6puSxLgQU-XKYzF1FB1qVe2o,8473
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toil-9.2.0.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
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toil-9.2.0.dist-info/entry_points.txt,sha256=EF2yFhV2UYuJGr-OjMkUOd3RyOCgRWQbS6XJtBJ25eM,436
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toil-9.2.0.dist-info/top_level.txt,sha256=1ydj7IXvHS9tMT5OVTSSpub6ZOaQeIn3KGCgJqaikF0,5
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toil/test/cwl/staging_cat.cwl
DELETED
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#!/usr/bin/env cwl-runner
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cwlVersion: v1.0
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DockerRequirement: # <- this is the part that causes the error
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InitialWorkDirRequirement:
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for i in \$(find some_dir -type f); do cat \$i ; done
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type: stdout
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@@ -1,25 +0,0 @@
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#!/usr/bin/env cwl-runner
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cwlVersion: v1.0
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sampleId:
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position: 1
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@@ -1,43 +0,0 @@
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#!/usr/bin/env cwl-runner
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cwlVersion: v1.0
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class: Workflow
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MultipleInputFeatureRequirement: {}
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ScatterFeatureRequirement: {}
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StepInputExpressionRequirement: {}
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SubworkflowFeatureRequirement: {}
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type:
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type: record
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sampleId: string
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make_file:
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run: staging_make_file.cwl
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scatter: sample
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in:
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sample: samples
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sampleId:
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valueFrom: ${ return inputs.sample['sampleId']; }
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out:
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[ output_file ]
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gather_files:
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run: staging_cat.cwl
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input_files: make_file/output_file
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[ output_file ]
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outputs:
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output_file:
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type: File
|
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42
|
-
outputSource: gather_files/output_file
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43
|
-
|
toil/test/cwl/zero_default.cwl
DELETED
|
@@ -1,61 +0,0 @@
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#!/usr/bin/env cwl-runner
|
|
2
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cwlVersion: v1.2
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class: Workflow
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requirements:
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MultipleInputFeatureRequirement: {}
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InlineJavascriptRequirement: {}
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|
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inputs:
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8
|
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valueA:
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|
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type: int?
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|
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default: 0
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valueB:
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type: int?
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someFile:
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type: File?
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|
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steps:
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prev_step:
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run:
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class: ExpressionTool
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requirements:
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InlineJavascriptRequirement: {}
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inputs:
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someFile:
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type: File
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outputs:
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|
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valueA:
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|
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type: int
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27
|
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expression: |
|
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28
|
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${
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29
|
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return {valueA: 1};
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|
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}
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31
|
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in:
|
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32
|
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someFile: someFile
|
|
33
|
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out: [valueA]
|
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34
|
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when: $(inputs.someFile != null)
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35
|
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|
36
|
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main_step:
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|
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run:
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|
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class: ExpressionTool
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|
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requirements:
|
|
40
|
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InlineJavascriptRequirement: {}
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|
41
|
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inputs:
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|
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valueA:
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type: int
|
|
44
|
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outputs:
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45
|
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valueA:
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type: int
|
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47
|
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expression: |
|
|
48
|
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${
|
|
49
|
-
return {valueA: inputs.valueA};
|
|
50
|
-
}
|
|
51
|
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in:
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|
52
|
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valueA:
|
|
53
|
-
source: [prev_step/valueA, valueA]
|
|
54
|
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pickValue: first_non_null
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55
|
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out: [valueA]
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56
|
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outputs:
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|
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valueA:
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58
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type: int
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59
|
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outputSource: main_step/valueA
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|
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@@ -1 +0,0 @@
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ABC
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File without changes
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