From 2c571efa6c8165814c95b1cd8867f84920792403 Mon Sep 17 00:00:00 2001 From: Rok Roskar <rok.roskar@sdsc.ethz.ch> Date: Thu, 27 May 2021 18:31:28 +0200 Subject: [PATCH] renku migrate: committing migrated workflow --- .renku/activity_index.yaml | 8 + .../483e40a495904a2288be9d726c9b92c5.cwl | 120 ----- ...9d0d6a6144fe83c567ead050ca2d_migrated.yaml | 434 ++++++++++++++++++ 3 files changed, 442 insertions(+), 120 deletions(-) delete mode 100644 .renku/workflow/483e40a495904a2288be9d726c9b92c5.cwl create mode 100644 .renku/workflow/f1089d0d6a6144fe83c567ead050ca2d_migrated.yaml diff --git a/.renku/activity_index.yaml b/.renku/activity_index.yaml index 00ebee2ab..ebe09e2ef 100644 --- a/.renku/activity_index.yaml +++ b/.renku/activity_index.yaml @@ -459,6 +459,8 @@ data/covidtracking: - .renku/workflow/52461ed667904a6e943e99305c4bbc66_migrated.yaml c155695195c2e03d83a201ff4b8156a16d503b69: - .renku/workflow/473c07fa033f4a10a7cc15d150e8ba86_migrated.yaml + c2470f1786204168b1c9184294a9754193c04d86: + - .renku/workflow/f1089d0d6a6144fe83c567ead050ca2d_migrated.yaml c25a44f3d7a46e38ffb94e04bb2b1a20e1682110: - .renku/workflow/9fbba023804f4f438b83e059adf67da4_migrated.yaml c292ceb84076cf5fc3056aaa62ef6eab1d9e90ff: @@ -937,6 +939,8 @@ data/covidtracking/states-daily.json: - .renku/workflow/52461ed667904a6e943e99305c4bbc66_migrated.yaml c155695195c2e03d83a201ff4b8156a16d503b69: - .renku/workflow/473c07fa033f4a10a7cc15d150e8ba86_migrated.yaml + c2470f1786204168b1c9184294a9754193c04d86: + - .renku/workflow/f1089d0d6a6144fe83c567ead050ca2d_migrated.yaml c25a44f3d7a46e38ffb94e04bb2b1a20e1682110: - .renku/workflow/9fbba023804f4f438b83e059adf67da4_migrated.yaml c292ceb84076cf5fc3056aaa62ef6eab1d9e90ff: @@ -1410,6 +1414,8 @@ data/covidtracking/states-metadata.json: - .renku/workflow/52461ed667904a6e943e99305c4bbc66_migrated.yaml c155695195c2e03d83a201ff4b8156a16d503b69: - .renku/workflow/473c07fa033f4a10a7cc15d150e8ba86_migrated.yaml + c2470f1786204168b1c9184294a9754193c04d86: + - .renku/workflow/f1089d0d6a6144fe83c567ead050ca2d_migrated.yaml c25a44f3d7a46e38ffb94e04bb2b1a20e1682110: - .renku/workflow/9fbba023804f4f438b83e059adf67da4_migrated.yaml c292ceb84076cf5fc3056aaa62ef6eab1d9e90ff: @@ -2890,6 +2896,8 @@ runs/download-covidtracking-data.runs.ipynb: - .renku/workflow/52461ed667904a6e943e99305c4bbc66_migrated.yaml c155695195c2e03d83a201ff4b8156a16d503b69: - .renku/workflow/473c07fa033f4a10a7cc15d150e8ba86_migrated.yaml + c2470f1786204168b1c9184294a9754193c04d86: + - .renku/workflow/f1089d0d6a6144fe83c567ead050ca2d_migrated.yaml c25a44f3d7a46e38ffb94e04bb2b1a20e1682110: - .renku/workflow/9fbba023804f4f438b83e059adf67da4_migrated.yaml c292ceb84076cf5fc3056aaa62ef6eab1d9e90ff: diff --git a/.renku/workflow/483e40a495904a2288be9d726c9b92c5.cwl b/.renku/workflow/483e40a495904a2288be9d726c9b92c5.cwl deleted file mode 100644 index e54b72880..000000000 --- a/.renku/workflow/483e40a495904a2288be9d726c9b92c5.cwl +++ /dev/null @@ -1,120 +0,0 @@ -class: Workflow -cwlVersion: v1.0 -hints: [] -inputs: - input_1: - default: states-daily.json - streamable: false - type: string - input_2: - default: states-metadata.json - streamable: false - type: string - input_3: - default: out_folder - streamable: false - type: string - input_4: - default: data/covidtracking - streamable: false - type: string - input_5: - default: - class: File - path: ../../notebooks/process/download-covidtracking-data.ipynb - streamable: false - type: File - input_6: - default: runs/download-covidtracking-data.runs.ipynb - streamable: false - type: string -outputs: - output_1: - outputSource: step_3/output_0 - streamable: false - type: File - output_2: - outputSource: step_3/output_1 - streamable: false - type: Directory -requirements: [] -steps: - step_1: - in: - filename: input_1 - input_directory: step_3/output_1 - out: - - output_file - run: - arguments: [] - baseCommand: - - 'true' - class: CommandLineTool - cwlVersion: v1.0 - hints: [] - inputs: - filename: - default: states-daily.json - streamable: false - type: string - input_directory: - streamable: false - type: Directory - outputs: - output_file: - outputBinding: - glob: $(inputs.filename) - streamable: false - type: File - permanentFailCodes: [] - requirements: - - &id001 - class: InlineJavascriptRequirement - - &id002 - class: InitialWorkDirRequirement - listing: $(inputs.input_directory.listing) - successCodes: [] - temporaryFailCodes: [] - step_2: - in: - filename: input_2 - input_directory: step_3/output_1 - out: - - output_file - run: - arguments: [] - baseCommand: - - 'true' - class: CommandLineTool - cwlVersion: v1.0 - hints: [] - inputs: - filename: - default: states-metadata.json - streamable: false - type: string - input_directory: - streamable: false - type: Directory - outputs: - output_file: - outputBinding: - glob: $(inputs.filename) - streamable: false - type: File - permanentFailCodes: [] - requirements: - - *id001 - - *id002 - successCodes: [] - temporaryFailCodes: [] - step_3: - in: - input_1: input_3 - input_2: input_4 - input_3: input_5 - input_4: input_6 - out: - - output_1 - - output_0 - run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl diff --git a/.renku/workflow/f1089d0d6a6144fe83c567ead050ca2d_migrated.yaml b/.renku/workflow/f1089d0d6a6144fe83c567ead050ca2d_migrated.yaml new file mode 100644 index 000000000..374e0f695 --- /dev/null +++ b/.renku/workflow/f1089d0d6a6144fe83c567ead050ca2d_migrated.yaml @@ -0,0 +1,434 @@ +- '@id': https://github.com/swissdatasciencecenter/renku-python/tree/v0.10.4 + '@type': + - http://purl.org/wf4ever/wfprov#WorkflowEngine + - http://www.w3.org/ns/prov#SoftwareAgent + http://www.w3.org/2000/01/rdf-schema#label: + - '@value': renku 0.10.4 +- '@id': https://github.com/swissdatasciencecenter/renku-python/tree/v0.15.1 + '@type': + - http://purl.org/wf4ever/wfprov#WorkflowEngine + - http://www.w3.org/ns/prov#SoftwareAgent + http://www.w3.org/2000/01/rdf-schema#label: + - '@value': renku 0.15.1 +- '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86 + '@type': + - http://purl.org/wf4ever/wfprov#ProcessRun + - http://purl.org/wf4ever/wfprov#WorkflowRun + - http://www.w3.org/ns/prov#Activity + http://schema.org/isPartOf: + - '@id': https://renkulab.io/projects/covid-19/covid-19-public-data + http://www.w3.org/2000/01/rdf-schema#comment: + - '@value': renku rerun data/covidtracking/states-metadata.json data/covidtracking/states-daily.json + http://www.w3.org/2000/01/rdf-schema#label: + - '@value': .renku/workflow/f1089d0d6a6144fe83c567ead050ca2d_migrated.yaml@c2470f1786204168b1c9184294a9754193c04d86 + http://www.w3.org/ns/prov#atLocation: + - '@value': .renku/workflow/f1089d0d6a6144fe83c567ead050ca2d_migrated.yaml + http://www.w3.org/ns/prov#endedAtTime: + - '@type': http://www.w3.org/2001/XMLSchema#dateTime + '@value': '2020-12-02T07:37:57+00:00' + http://www.w3.org/ns/prov#influenced: [] + http://www.w3.org/ns/prov#qualifiedAssociation: + - '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86/association + http://www.w3.org/ns/prov#qualifiedUsage: + - '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86/inputs/1 + http://www.w3.org/ns/prov#startedAtTime: + - '@type': http://www.w3.org/2001/XMLSchema#dateTime + '@value': '2020-12-02T07:37:57+00:00' + http://www.w3.org/ns/prov#wasAssociatedWith: + - '@id': mailto:beepbop@example.com + - '@id': https://github.com/swissdatasciencecenter/renku-python/tree/v0.15.1 + http://www.w3.org/ns/prov#wasInformedBy: + - '@id': https://localhost/activities/commit/1c2ccfb6dc4503b4808b064f7e130f5e78cd33f4 +- '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86/association + '@type': + - http://www.w3.org/ns/prov#Association + http://www.w3.org/ns/prov#agent: + - '@id': https://github.com/swissdatasciencecenter/renku-python/tree/v0.10.4 + http://www.w3.org/ns/prov#hadPlan: + - '@id': https://renkulab.io/runs/1b2a4a42fa1897abfbc7c25c93d19a2615db8773 +- '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86/inputs/1 + '@type': + - http://www.w3.org/ns/prov#Usage + http://www.w3.org/ns/prov#entity: + - '@id': https://renkulab.io/blob/d754df040a4bf8f7cb7ae6ed4151830f9bb0f520/notebooks/process/download-covidtracking-data.ipynb + http://www.w3.org/ns/prov#hadRole: + - '@value': steps/step_1/inputs/3 +- '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86/steps/step_1 + '@type': + - http://purl.org/wf4ever/wfprov#ProcessRun + - http://www.w3.org/ns/prov#Activity + http://purl.org/wf4ever/wfprov#wasPartOfWorkflowRun: + - '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86 + http://schema.org/isPartOf: + - '@id': https://renkulab.io/projects/covid-19/covid-19-public-data + http://www.w3.org/2000/01/rdf-schema#comment: + - '@value': renku rerun data/covidtracking/states-metadata.json data/covidtracking/states-daily.json + http://www.w3.org/2000/01/rdf-schema#label: + - '@value': .renku/workflow/f1089d0d6a6144fe83c567ead050ca2d_migrated.yaml@c2470f1786204168b1c9184294a9754193c04d86 + http://www.w3.org/ns/prov#atLocation: + - '@value': .renku/workflow/f1089d0d6a6144fe83c567ead050ca2d_migrated.yaml + http://www.w3.org/ns/prov#endedAtTime: + - '@type': http://www.w3.org/2001/XMLSchema#dateTime + '@value': '2020-12-02T07:37:57+00:00' + http://www.w3.org/ns/prov#influenced: [] + http://www.w3.org/ns/prov#qualifiedAssociation: + - '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86/steps/step_1/association + http://www.w3.org/ns/prov#qualifiedUsage: + - '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86/steps/step_1/inputs/3 + http://www.w3.org/ns/prov#startedAtTime: + - '@type': http://www.w3.org/2001/XMLSchema#dateTime + '@value': '2020-12-02T07:37:57+00:00' + http://www.w3.org/ns/prov#wasAssociatedWith: + - '@id': mailto:beepbop@example.com + - '@id': https://github.com/swissdatasciencecenter/renku-python/tree/v0.15.1 + http://www.w3.org/ns/prov#wasInformedBy: + - '@id': https://localhost/activities/commit/1c2ccfb6dc4503b4808b064f7e130f5e78cd33f4 + https://swissdatasciencecenter.github.io/renku-ontology#hasRunParameter: [] +- '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86/steps/step_1/association + '@type': + - http://www.w3.org/ns/prov#Association + http://www.w3.org/ns/prov#agent: + - '@id': https://github.com/swissdatasciencecenter/renku-python/tree/v0.10.4 + http://www.w3.org/ns/prov#hadPlan: + - '@id': https://renkulab.io/runs/e602640613eb60e3dce9191e87253dc9e37c8e38 +- '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86/steps/step_1/inputs/3 + '@type': + - http://www.w3.org/ns/prov#Usage + http://www.w3.org/ns/prov#entity: + - '@id': https://renkulab.io/blob/d754df040a4bf8f7cb7ae6ed4151830f9bb0f520/notebooks/process/download-covidtracking-data.ipynb + http://www.w3.org/ns/prov#hadRole: + - '@value': inputs/3 +- '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86/steps/step_1/outputs/2 + '@type': + - http://www.w3.org/ns/prov#Generation + http://www.w3.org/ns/prov#activity: + - '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86/steps/step_1 + - '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86 + http://www.w3.org/ns/prov#hadRole: + - '@value': outputs/2 +- '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86/steps/step_1/outputs/4 + '@type': + - http://www.w3.org/ns/prov#Generation + http://www.w3.org/ns/prov#activity: + - '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86/steps/step_1 + - '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86 + http://www.w3.org/ns/prov#hadRole: + - '@value': outputs/4 +- '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86/steps/step_1/tree/data/covidtracking/states-daily.json + '@type': + - http://www.w3.org/ns/prov#Generation + http://www.w3.org/ns/prov#activity: + - '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86 +- '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86/steps/step_1/tree/data/covidtracking/states-metadata.json + '@type': + - http://www.w3.org/ns/prov#Generation + http://www.w3.org/ns/prov#activity: + - '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86 +- '@id': https://renkulab.io/blob/c2470f1786204168b1c9184294a9754193c04d86/data/covidtracking + '@type': + - http://purl.org/wf4ever/wfprov#Artifact + - http://www.w3.org/ns/prov#Collection + - http://www.w3.org/ns/prov#Entity + http://schema.org/isPartOf: + - '@id': https://renkulab.io/projects/covid-19/covid-19-public-data + http://www.w3.org/2000/01/rdf-schema#label: + - '@value': data/covidtracking@c2470f1786204168b1c9184294a9754193c04d86 + http://www.w3.org/ns/prov#atLocation: + - '@value': data/covidtracking + http://www.w3.org/ns/prov#hadMember: + - '@id': https://renkulab.io/blob/c2470f1786204168b1c9184294a9754193c04d86/data/covidtracking/states-daily.json + - '@id': https://renkulab.io/blob/c2470f1786204168b1c9184294a9754193c04d86/data/covidtracking/states-metadata.json + http://www.w3.org/ns/prov#qualifiedGeneration: + - '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86/steps/step_1/outputs/2 +- '@id': https://renkulab.io/blob/c2470f1786204168b1c9184294a9754193c04d86/data/covidtracking/states-daily.json + '@type': + - http://purl.org/wf4ever/wfprov#Artifact + - http://www.w3.org/ns/prov#Entity + http://schema.org/isPartOf: + - '@id': https://renkulab.io/projects/covid-19/covid-19-public-data + http://www.w3.org/2000/01/rdf-schema#label: + - '@value': data/covidtracking/states-daily.json@c2470f1786204168b1c9184294a9754193c04d86 + http://www.w3.org/ns/prov#atLocation: + - '@value': data/covidtracking/states-daily.json + http://www.w3.org/ns/prov#qualifiedGeneration: + - '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86/steps/step_1/tree/data/covidtracking/states-daily.json +- '@id': https://renkulab.io/blob/c2470f1786204168b1c9184294a9754193c04d86/data/covidtracking/states-metadata.json + '@type': + - http://purl.org/wf4ever/wfprov#Artifact + - http://www.w3.org/ns/prov#Entity + http://schema.org/isPartOf: + - '@id': https://renkulab.io/projects/covid-19/covid-19-public-data + http://www.w3.org/2000/01/rdf-schema#label: + - '@value': data/covidtracking/states-metadata.json@c2470f1786204168b1c9184294a9754193c04d86 + http://www.w3.org/ns/prov#atLocation: + - '@value': data/covidtracking/states-metadata.json + http://www.w3.org/ns/prov#qualifiedGeneration: + - '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86/steps/step_1/tree/data/covidtracking/states-metadata.json +- '@id': https://renkulab.io/blob/c2470f1786204168b1c9184294a9754193c04d86/runs/download-covidtracking-data.runs.ipynb + '@type': + - http://purl.org/wf4ever/wfprov#Artifact + - http://www.w3.org/ns/prov#Entity + http://schema.org/isPartOf: + - '@id': https://renkulab.io/projects/covid-19/covid-19-public-data + http://www.w3.org/2000/01/rdf-schema#label: + - '@value': runs/download-covidtracking-data.runs.ipynb@c2470f1786204168b1c9184294a9754193c04d86 + http://www.w3.org/ns/prov#atLocation: + - '@value': runs/download-covidtracking-data.runs.ipynb + http://www.w3.org/ns/prov#qualifiedGeneration: + - '@id': https://localhost/activities/commit/c2470f1786204168b1c9184294a9754193c04d86/steps/step_1/outputs/4 +- '@id': https://renkulab.io/blob/ccc37edffe6d9ca8ea4b8a229d1d20c42bc4b658/data/covidtracking + '@type': + - http://purl.org/wf4ever/wfprov#Artifact + - http://www.w3.org/ns/prov#Collection + - http://www.w3.org/ns/prov#Entity + http://schema.org/isPartOf: + - '@id': https://renkulab.io/projects/covid-19/covid-19-public-data + http://www.w3.org/2000/01/rdf-schema#label: + - '@value': data/covidtracking@ccc37edffe6d9ca8ea4b8a229d1d20c42bc4b658 + http://www.w3.org/ns/prov#atLocation: + - '@value': data/covidtracking + http://www.w3.org/ns/prov#hadMember: + - '@id': https://renkulab.io/blob/ccc37edffe6d9ca8ea4b8a229d1d20c42bc4b658/data/covidtracking/states-daily.json + - '@id': https://renkulab.io/blob/ccc37edffe6d9ca8ea4b8a229d1d20c42bc4b658/data/covidtracking/states-metadata.json +- '@id': https://renkulab.io/blob/ccc37edffe6d9ca8ea4b8a229d1d20c42bc4b658/data/covidtracking/states-daily.json + '@type': + - http://purl.org/wf4ever/wfprov#Artifact + - http://www.w3.org/ns/prov#Entity + http://schema.org/isPartOf: + - '@id': https://renkulab.io/projects/covid-19/covid-19-public-data + http://www.w3.org/2000/01/rdf-schema#label: + - '@value': data/covidtracking/states-daily.json@ccc37edffe6d9ca8ea4b8a229d1d20c42bc4b658 + http://www.w3.org/ns/prov#atLocation: + - '@value': data/covidtracking/states-daily.json +- '@id': https://renkulab.io/blob/ccc37edffe6d9ca8ea4b8a229d1d20c42bc4b658/data/covidtracking/states-metadata.json + '@type': + - http://purl.org/wf4ever/wfprov#Artifact + - 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