From 5ac35a0342b2d8d482867eeb3a843f40fe3974b7 Mon Sep 17 00:00:00 2001 From: Rok Roskar <rok.roskar@sdsc.ethz.ch> Date: Thu, 27 May 2021 18:24:42 +0200 Subject: [PATCH] renku migrate: committing migrated workflow --- .renku/activity_index.yaml | 8 + .../131c8c06eb2a49a881e084d0059d2f4f.cwl | 120 ----- ...adb07ab043579abfff5b98628253_migrated.yaml | 434 ++++++++++++++++++ 3 files changed, 442 insertions(+), 120 deletions(-) delete mode 100644 .renku/workflow/131c8c06eb2a49a881e084d0059d2f4f.cwl create mode 100644 .renku/workflow/a3c0adb07ab043579abfff5b98628253_migrated.yaml diff --git a/.renku/activity_index.yaml b/.renku/activity_index.yaml index 997b5192c..29e8a8fb0 100644 --- a/.renku/activity_index.yaml +++ b/.renku/activity_index.yaml @@ -407,6 +407,8 @@ data/covidtracking: - .renku/workflow/473c07fa033f4a10a7cc15d150e8ba86_migrated.yaml c292ceb84076cf5fc3056aaa62ef6eab1d9e90ff: - .renku/workflow/5e9b323c62254515bc89b25172cf1c4f_migrated.yaml + c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20: + - .renku/workflow/a3c0adb07ab043579abfff5b98628253_migrated.yaml c41914b8c268fefbe02a83efeca6383b869e6b7c: - .renku/workflow/de7ea086c3c241289aa0a9f89783dd4e_migrated.yaml c4a3a9b295cbbe268a8c086e9dc30385ee1b6046: @@ -813,6 +815,8 @@ data/covidtracking/states-daily.json: - .renku/workflow/473c07fa033f4a10a7cc15d150e8ba86_migrated.yaml c292ceb84076cf5fc3056aaa62ef6eab1d9e90ff: - .renku/workflow/5e9b323c62254515bc89b25172cf1c4f_migrated.yaml + c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20: + - .renku/workflow/a3c0adb07ab043579abfff5b98628253_migrated.yaml c41914b8c268fefbe02a83efeca6383b869e6b7c: - .renku/workflow/de7ea086c3c241289aa0a9f89783dd4e_migrated.yaml c4a3a9b295cbbe268a8c086e9dc30385ee1b6046: @@ -1214,6 +1218,8 @@ data/covidtracking/states-metadata.json: - .renku/workflow/473c07fa033f4a10a7cc15d150e8ba86_migrated.yaml c292ceb84076cf5fc3056aaa62ef6eab1d9e90ff: - .renku/workflow/5e9b323c62254515bc89b25172cf1c4f_migrated.yaml + c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20: + - .renku/workflow/a3c0adb07ab043579abfff5b98628253_migrated.yaml c41914b8c268fefbe02a83efeca6383b869e6b7c: - .renku/workflow/de7ea086c3c241289aa0a9f89783dd4e_migrated.yaml c4a3a9b295cbbe268a8c086e9dc30385ee1b6046: @@ -2568,6 +2574,8 @@ runs/download-covidtracking-data.runs.ipynb: - .renku/workflow/473c07fa033f4a10a7cc15d150e8ba86_migrated.yaml c292ceb84076cf5fc3056aaa62ef6eab1d9e90ff: - .renku/workflow/5e9b323c62254515bc89b25172cf1c4f_migrated.yaml + c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20: + - .renku/workflow/a3c0adb07ab043579abfff5b98628253_migrated.yaml c41914b8c268fefbe02a83efeca6383b869e6b7c: - .renku/workflow/de7ea086c3c241289aa0a9f89783dd4e_migrated.yaml c4a3a9b295cbbe268a8c086e9dc30385ee1b6046: diff --git a/.renku/workflow/131c8c06eb2a49a881e084d0059d2f4f.cwl b/.renku/workflow/131c8c06eb2a49a881e084d0059d2f4f.cwl deleted file mode 100644 index 4dfcafb5b..000000000 --- a/.renku/workflow/131c8c06eb2a49a881e084d0059d2f4f.cwl +++ /dev/null @@ -1,120 +0,0 @@ -class: Workflow -cwlVersion: v1.0 -hints: [] -inputs: - input_1: - default: out_folder - streamable: false - type: string - input_2: - default: data/covidtracking - streamable: false - type: string - input_3: - default: - class: File - path: ../../notebooks/process/download-covidtracking-data.ipynb - streamable: false - type: File - input_4: - default: runs/download-covidtracking-data.runs.ipynb - streamable: false - type: string - input_5: - default: states-metadata.json - streamable: false - type: string - input_6: - default: states-daily.json - streamable: false - type: string -outputs: - output_0: - outputSource: step_1/output_1 - streamable: false - type: Directory - output_3: - outputSource: step_1/output_0 - streamable: false - type: File -requirements: [] -steps: - step_1: - in: - input_1: input_1 - input_2: input_2 - input_3: input_3 - input_4: input_4 - out: - - output_1 - - output_0 - run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl - step_2: - in: - filename: input_5 - input_directory: step_1/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 - class: InlineJavascriptRequirement - - &id002 - class: InitialWorkDirRequirement - listing: $(inputs.input_directory.listing) - successCodes: [] - temporaryFailCodes: [] - step_3: - in: - filename: input_6 - input_directory: step_1/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 - - *id002 - successCodes: [] - temporaryFailCodes: [] diff --git a/.renku/workflow/a3c0adb07ab043579abfff5b98628253_migrated.yaml b/.renku/workflow/a3c0adb07ab043579abfff5b98628253_migrated.yaml new file mode 100644 index 000000000..92870d31c --- /dev/null +++ b/.renku/workflow/a3c0adb07ab043579abfff5b98628253_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/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20 + '@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/a3c0adb07ab043579abfff5b98628253_migrated.yaml@c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20 + http://www.w3.org/ns/prov#atLocation: + - '@value': .renku/workflow/a3c0adb07ab043579abfff5b98628253_migrated.yaml + http://www.w3.org/ns/prov#endedAtTime: + - '@type': http://www.w3.org/2001/XMLSchema#dateTime + '@value': '2020-10-26T07:38:12+00:00' + http://www.w3.org/ns/prov#influenced: [] + http://www.w3.org/ns/prov#qualifiedAssociation: + - '@id': https://localhost/activities/commit/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/association + http://www.w3.org/ns/prov#qualifiedUsage: + - '@id': https://localhost/activities/commit/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/inputs/1 + http://www.w3.org/ns/prov#startedAtTime: + - '@type': http://www.w3.org/2001/XMLSchema#dateTime + '@value': '2020-10-26T07:38:12+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/ebafdd41cf77ed14ed351842cf90dc6081862fbb +- '@id': https://localhost/activities/commit/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/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/2fb50ca7a235e0d5b0dd3a2fda16fb3b4ac289e2 +- '@id': https://localhost/activities/commit/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/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/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/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/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20 + 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/a3c0adb07ab043579abfff5b98628253_migrated.yaml@c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20 + http://www.w3.org/ns/prov#atLocation: + - '@value': .renku/workflow/a3c0adb07ab043579abfff5b98628253_migrated.yaml + http://www.w3.org/ns/prov#endedAtTime: + - '@type': http://www.w3.org/2001/XMLSchema#dateTime + '@value': '2020-10-26T07:38:12+00:00' + http://www.w3.org/ns/prov#influenced: [] + http://www.w3.org/ns/prov#qualifiedAssociation: + - '@id': https://localhost/activities/commit/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/steps/step_1/association + http://www.w3.org/ns/prov#qualifiedUsage: + - '@id': https://localhost/activities/commit/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/steps/step_1/inputs/3 + http://www.w3.org/ns/prov#startedAtTime: + - '@type': http://www.w3.org/2001/XMLSchema#dateTime + '@value': '2020-10-26T07:38:12+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/ebafdd41cf77ed14ed351842cf90dc6081862fbb + https://swissdatasciencecenter.github.io/renku-ontology#hasRunParameter: [] +- '@id': https://localhost/activities/commit/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/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/072a75fdff897361e9f23ac4683700d4ac2f9d13 +- '@id': https://localhost/activities/commit/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/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/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/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/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/steps/step_1 + - '@id': https://localhost/activities/commit/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20 + http://www.w3.org/ns/prov#hadRole: + - '@value': outputs/2 +- '@id': https://localhost/activities/commit/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/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/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/steps/step_1 + - '@id': https://localhost/activities/commit/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20 + http://www.w3.org/ns/prov#hadRole: + - '@value': outputs/4 +- '@id': https://localhost/activities/commit/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/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/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20 +- '@id': https://localhost/activities/commit/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/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/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20 +- '@id': https://renkulab.io/blob/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/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@c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20 + http://www.w3.org/ns/prov#atLocation: + - '@value': data/covidtracking + http://www.w3.org/ns/prov#hadMember: + - '@id': https://renkulab.io/blob/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/data/covidtracking/states-daily.json + - '@id': https://renkulab.io/blob/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/data/covidtracking/states-metadata.json + http://www.w3.org/ns/prov#qualifiedGeneration: + - '@id': https://localhost/activities/commit/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/steps/step_1/outputs/2 +- '@id': https://renkulab.io/blob/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/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@c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20 + 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/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/steps/step_1/tree/data/covidtracking/states-daily.json +- '@id': https://renkulab.io/blob/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/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@c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20 + 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/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/steps/step_1/tree/data/covidtracking/states-metadata.json +- '@id': https://renkulab.io/blob/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/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@c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20 + 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/c38af6f655d24c2ea5e00f1b4ea159f4aaa3ef20/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: + - 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