From b16a85f70c7c3d946e97ea7807b8e234fe55174a Mon Sep 17 00:00:00 2001 From: Rok Roskar <rok.roskar@sdsc.ethz.ch> Date: Thu, 27 May 2021 18:25:27 +0200 Subject: [PATCH] renku migrate: committing migrated workflow --- .renku/activity_index.yaml | 8 + .../050e8f458e484c0281c4846de954afc4.cwl | 120 ----- ...ecc72594429a96c887aa1aeaccf3_migrated.yaml | 434 ++++++++++++++++++ 3 files changed, 442 insertions(+), 120 deletions(-) delete mode 100644 .renku/workflow/050e8f458e484c0281c4846de954afc4.cwl create mode 100644 .renku/workflow/4d4becc72594429a96c887aa1aeaccf3_migrated.yaml diff --git a/.renku/activity_index.yaml b/.renku/activity_index.yaml index 3e233cba0..89f179799 100644 --- a/.renku/activity_index.yaml +++ b/.renku/activity_index.yaml @@ -460,6 +460,8 @@ data/covidtracking: - .renku/workflow/997b166b69104229ac2c1f59b0de2238_migrated.yaml d8d021db9c57c1178f4577514b069df007c96101: - .renku/workflow/be05ba1d3be3484cbd13e615d578e294_migrated.yaml + d8e1c589c3d5b20605c4e4f279688f9892efa863: + - .renku/workflow/4d4becc72594429a96c887aa1aeaccf3_migrated.yaml dadaeaeca1cef285c48fd093c3c400c74bbae9d7: - .renku/workflow/2ac3eb9884774070ae469bb92def2699_migrated.yaml dc210a37569028d9c48b875b623df164ba0e63ce: @@ -885,6 +887,8 @@ data/covidtracking/states-daily.json: - .renku/workflow/997b166b69104229ac2c1f59b0de2238_migrated.yaml d8d021db9c57c1178f4577514b069df007c96101: - .renku/workflow/be05ba1d3be3484cbd13e615d578e294_migrated.yaml + d8e1c589c3d5b20605c4e4f279688f9892efa863: + - .renku/workflow/4d4becc72594429a96c887aa1aeaccf3_migrated.yaml dadaeaeca1cef285c48fd093c3c400c74bbae9d7: - .renku/workflow/2ac3eb9884774070ae469bb92def2699_migrated.yaml dc210a37569028d9c48b875b623df164ba0e63ce: @@ -1308,6 +1312,8 @@ data/covidtracking/states-metadata.json: - .renku/workflow/997b166b69104229ac2c1f59b0de2238_migrated.yaml d8d021db9c57c1178f4577514b069df007c96101: - .renku/workflow/be05ba1d3be3484cbd13e615d578e294_migrated.yaml + d8e1c589c3d5b20605c4e4f279688f9892efa863: + - .renku/workflow/4d4becc72594429a96c887aa1aeaccf3_migrated.yaml dadaeaeca1cef285c48fd093c3c400c74bbae9d7: - .renku/workflow/2ac3eb9884774070ae469bb92def2699_migrated.yaml dc210a37569028d9c48b875b623df164ba0e63ce: @@ -2704,6 +2710,8 @@ runs/download-covidtracking-data.runs.ipynb: - .renku/workflow/997b166b69104229ac2c1f59b0de2238_migrated.yaml d8d021db9c57c1178f4577514b069df007c96101: - .renku/workflow/be05ba1d3be3484cbd13e615d578e294_migrated.yaml + d8e1c589c3d5b20605c4e4f279688f9892efa863: + - .renku/workflow/4d4becc72594429a96c887aa1aeaccf3_migrated.yaml dadaeaeca1cef285c48fd093c3c400c74bbae9d7: - .renku/workflow/2ac3eb9884774070ae469bb92def2699_migrated.yaml dc210a37569028d9c48b875b623df164ba0e63ce: diff --git a/.renku/workflow/050e8f458e484c0281c4846de954afc4.cwl b/.renku/workflow/050e8f458e484c0281c4846de954afc4.cwl deleted file mode 100644 index a0067321b..000000000 --- a/.renku/workflow/050e8f458e484c0281c4846de954afc4.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: out_folder - streamable: false - type: string - input_3: - default: data/covidtracking - streamable: false - type: string - input_4: - default: - class: File - path: ../../notebooks/process/download-covidtracking-data.ipynb - streamable: false - type: File - input_5: - default: runs/download-covidtracking-data.runs.ipynb - streamable: false - type: string - input_6: - default: states-metadata.json - streamable: false - type: string -outputs: - output_1: - outputSource: step_2/output_1 - streamable: false - type: Directory - output_2: - outputSource: step_2/output_0 - streamable: false - type: File -requirements: [] -steps: - step_1: - in: - filename: input_1 - input_directory: step_2/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: - input_1: input_2 - input_2: input_3 - input_3: input_4 - input_4: input_5 - out: - - output_1 - - output_0 - run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl - step_3: - in: - filename: input_6 - input_directory: step_2/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: [] diff --git a/.renku/workflow/4d4becc72594429a96c887aa1aeaccf3_migrated.yaml b/.renku/workflow/4d4becc72594429a96c887aa1aeaccf3_migrated.yaml new file mode 100644 index 000000000..b640e9d1d --- /dev/null +++ b/.renku/workflow/4d4becc72594429a96c887aa1aeaccf3_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/d8e1c589c3d5b20605c4e4f279688f9892efa863 + '@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/4d4becc72594429a96c887aa1aeaccf3_migrated.yaml@d8e1c589c3d5b20605c4e4f279688f9892efa863 + http://www.w3.org/ns/prov#atLocation: + - '@value': .renku/workflow/4d4becc72594429a96c887aa1aeaccf3_migrated.yaml + http://www.w3.org/ns/prov#endedAtTime: + - '@type': http://www.w3.org/2001/XMLSchema#dateTime + '@value': '2020-11-06T07:36:20+00:00' + http://www.w3.org/ns/prov#influenced: [] + http://www.w3.org/ns/prov#qualifiedAssociation: + - '@id': https://localhost/activities/commit/d8e1c589c3d5b20605c4e4f279688f9892efa863/association + http://www.w3.org/ns/prov#qualifiedUsage: + - '@id': https://localhost/activities/commit/d8e1c589c3d5b20605c4e4f279688f9892efa863/inputs/1 + http://www.w3.org/ns/prov#startedAtTime: + - '@type': http://www.w3.org/2001/XMLSchema#dateTime + '@value': '2020-11-06T07:36:20+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/dc93d98fc7627b5fda03f2b12232ac5b66fffe34 +- '@id': https://localhost/activities/commit/d8e1c589c3d5b20605c4e4f279688f9892efa863/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/4acad4bcbcf23d27abf0162bdb724f273fb6fffe +- '@id': https://localhost/activities/commit/d8e1c589c3d5b20605c4e4f279688f9892efa863/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/d8e1c589c3d5b20605c4e4f279688f9892efa863/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/d8e1c589c3d5b20605c4e4f279688f9892efa863 + 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/4d4becc72594429a96c887aa1aeaccf3_migrated.yaml@d8e1c589c3d5b20605c4e4f279688f9892efa863 + http://www.w3.org/ns/prov#atLocation: + - '@value': .renku/workflow/4d4becc72594429a96c887aa1aeaccf3_migrated.yaml + http://www.w3.org/ns/prov#endedAtTime: + - '@type': http://www.w3.org/2001/XMLSchema#dateTime + '@value': '2020-11-06T07:36:20+00:00' + http://www.w3.org/ns/prov#influenced: [] + http://www.w3.org/ns/prov#qualifiedAssociation: + - '@id': https://localhost/activities/commit/d8e1c589c3d5b20605c4e4f279688f9892efa863/steps/step_1/association + http://www.w3.org/ns/prov#qualifiedUsage: + - '@id': https://localhost/activities/commit/d8e1c589c3d5b20605c4e4f279688f9892efa863/steps/step_1/inputs/3 + http://www.w3.org/ns/prov#startedAtTime: + - '@type': http://www.w3.org/2001/XMLSchema#dateTime + '@value': '2020-11-06T07:36:20+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/dc93d98fc7627b5fda03f2b12232ac5b66fffe34 + https://swissdatasciencecenter.github.io/renku-ontology#hasRunParameter: [] +- '@id': https://localhost/activities/commit/d8e1c589c3d5b20605c4e4f279688f9892efa863/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/32140ed32de31f75ae38c0215aa73f424a4dac9b +- '@id': https://localhost/activities/commit/d8e1c589c3d5b20605c4e4f279688f9892efa863/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/d8e1c589c3d5b20605c4e4f279688f9892efa863/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/d8e1c589c3d5b20605c4e4f279688f9892efa863/steps/step_1 + - '@id': https://localhost/activities/commit/d8e1c589c3d5b20605c4e4f279688f9892efa863 + http://www.w3.org/ns/prov#hadRole: + - '@value': outputs/2 +- '@id': https://localhost/activities/commit/d8e1c589c3d5b20605c4e4f279688f9892efa863/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/d8e1c589c3d5b20605c4e4f279688f9892efa863/steps/step_1 + - '@id': https://localhost/activities/commit/d8e1c589c3d5b20605c4e4f279688f9892efa863 + http://www.w3.org/ns/prov#hadRole: + - '@value': outputs/4 +- '@id': https://localhost/activities/commit/d8e1c589c3d5b20605c4e4f279688f9892efa863/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/d8e1c589c3d5b20605c4e4f279688f9892efa863 +- '@id': https://localhost/activities/commit/d8e1c589c3d5b20605c4e4f279688f9892efa863/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/d8e1c589c3d5b20605c4e4f279688f9892efa863 +- '@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 + - 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@ccc37edffe6d9ca8ea4b8a229d1d20c42bc4b658 + http://www.w3.org/ns/prov#atLocation: + - '@value': data/covidtracking/states-metadata.json +- '@id': https://renkulab.io/blob/ccc37edffe6d9ca8ea4b8a229d1d20c42bc4b658/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@ccc37edffe6d9ca8ea4b8a229d1d20c42bc4b658 + http://www.w3.org/ns/prov#atLocation: + - '@value': runs/download-covidtracking-data.runs.ipynb +- '@id': https://renkulab.io/blob/d754df040a4bf8f7cb7ae6ed4151830f9bb0f520/notebooks/process/download-covidtracking-data.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': notebooks/process/download-covidtracking-data.ipynb@d754df040a4bf8f7cb7ae6ed4151830f9bb0f520 + http://www.w3.org/ns/prov#atLocation: + - '@value': notebooks/process/download-covidtracking-data.ipynb +- '@id': https://renkulab.io/blob/d8e1c589c3d5b20605c4e4f279688f9892efa863/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: + - 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