From 0b4d2f69e9379fa678c444b8effae157e5c70a3a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rok=20Ro=C5=A1kar?= <rok.roskar@sdsc.ethz.ch>
Date: Thu, 26 Mar 2020 14:05:49 +0000
Subject: [PATCH] renku run --input
data/ch-population-statistics/ch-population-by-age-canton.xls papermill
--report-mode notebooks/openzh-covid-19-dashboard.ipynb
runs/openzh-covid-19-dashboard.run.ipynb -p data_path data/openzh-covid-19/
---
...b23203ef422185f0ecf77290cbd3_papermill.cwl | 77 +++++++++++++++
runs/openzh-covid-19-dashboard.run.ipynb | 96 +++++++++----------
2 files changed, 125 insertions(+), 48 deletions(-)
create mode 100644 .renku/workflow/0415b23203ef422185f0ecf77290cbd3_papermill.cwl
diff --git a/.renku/workflow/0415b23203ef422185f0ecf77290cbd3_papermill.cwl b/.renku/workflow/0415b23203ef422185f0ecf77290cbd3_papermill.cwl
new file mode 100644
index 00000000..c1a222f3
--- /dev/null
+++ b/.renku/workflow/0415b23203ef422185f0ecf77290cbd3_papermill.cwl
@@ -0,0 +1,77 @@
+arguments: []
+baseCommand:
+- papermill
+class: CommandLineTool
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default:
+ class: File
+ path: ../../notebooks/openzh-covid-19-dashboard.ipynb
+ inputBinding:
+ position: 1
+ prefix: --report-mode
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: File
+ input_2:
+ default: runs/openzh-covid-19-dashboard.run.ipynb
+ inputBinding:
+ position: 2
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_3:
+ default: data_path
+ inputBinding:
+ position: 3
+ prefix: -p
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_4:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/openzh-covid-19
+ inputBinding:
+ position: 4
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: Directory
+ input_5:
+ default:
+ class: File
+ path: ../../data/ch-population-statistics/ch-population-by-age-canton.xls
+ streamable: false
+ type: File
+outputs:
+ output_0:
+ outputBinding:
+ glob: $(inputs.input_2)
+ streamable: false
+ type: File
+permanentFailCodes: []
+requirements:
+- class: InlineJavascriptRequirement
+- class: InitialWorkDirRequirement
+ listing:
+ - entry: '$({"listing": [], "class": "Directory"})'
+ entryname: runs
+ writable: true
+ - entry: $(inputs.input_1)
+ entryname: notebooks/openzh-covid-19-dashboard.ipynb
+ writable: false
+ - entry: $(inputs.input_4)
+ entryname: data/openzh-covid-19
+ writable: false
+ - entry: $(inputs.input_5)
+ entryname: data/ch-population-statistics/ch-population-by-age-canton.xls
+ writable: false
+successCodes: []
+temporaryFailCodes: []
diff --git a/runs/openzh-covid-19-dashboard.run.ipynb b/runs/openzh-covid-19-dashboard.run.ipynb
index 6a84b3ce..a985c547 100644
--- a/runs/openzh-covid-19-dashboard.run.ipynb
+++ b/runs/openzh-covid-19-dashboard.run.ipynb
@@ -8,10 +8,10 @@
"source_hidden": true
},
"papermill": {
- "duration": 0.509865,
- "end_time": "2020-03-25T08:24:26.989132",
+ "duration": 0.553898,
+ "end_time": "2020-03-26T14:05:22.248651",
"exception": false,
- "start_time": "2020-03-25T08:24:26.479267",
+ "start_time": "2020-03-26T14:05:21.694753",
"status": "completed"
},
"tags": []
@@ -33,10 +33,10 @@
"source_hidden": true
},
"papermill": {
- "duration": 0.018076,
- "end_time": "2020-03-25T08:24:27.017436",
+ "duration": 0.020497,
+ "end_time": "2020-03-26T14:05:22.284973",
"exception": false,
- "start_time": "2020-03-25T08:24:26.999360",
+ "start_time": "2020-03-26T14:05:22.264476",
"status": "completed"
},
"tags": [
@@ -57,10 +57,10 @@
"source_hidden": true
},
"papermill": {
- "duration": 0.019273,
- "end_time": "2020-03-25T08:24:27.046078",
+ "duration": 0.020876,
+ "end_time": "2020-03-26T14:05:22.313009",
"exception": false,
- "start_time": "2020-03-25T08:24:27.026805",
+ "start_time": "2020-03-26T14:05:22.292133",
"status": "completed"
},
"tags": [
@@ -70,7 +70,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "data_path = \"/tmp/mz1u59o4/data/openzh-covid-19\"\n"
+ "data_path = \"data/openzh-covid-19/\"\n"
]
},
{
@@ -81,10 +81,10 @@
"source_hidden": true
},
"papermill": {
- "duration": 0.01949,
- "end_time": "2020-03-25T08:24:27.075345",
+ "duration": 0.021661,
+ "end_time": "2020-03-26T14:05:22.344850",
"exception": false,
- "start_time": "2020-03-25T08:24:27.055855",
+ "start_time": "2020-03-26T14:05:22.323189",
"status": "completed"
},
"tags": []
@@ -105,10 +105,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008491,
- "end_time": "2020-03-25T08:24:27.092431",
+ "duration": 0.007381,
+ "end_time": "2020-03-26T14:05:22.361234",
"exception": false,
- "start_time": "2020-03-25T08:24:27.083940",
+ "start_time": "2020-03-26T14:05:22.353853",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"source_hidden": true
},
"papermill": {
- "duration": 0.150486,
- "end_time": "2020-03-25T08:24:27.251462",
+ "duration": 0.133531,
+ "end_time": "2020-03-26T14:05:22.501475",
"exception": false,
- "start_time": "2020-03-25T08:24:27.100976",
+ "start_time": "2020-03-26T14:05:22.367944",
"status": "completed"
},
"tags": []
@@ -158,10 +158,10 @@
"source_hidden": true
},
"papermill": {
- "duration": 27.229887,
- "end_time": "2020-03-25T08:24:54.495573",
+ "duration": 26.113763,
+ "end_time": "2020-03-26T14:05:48.629957",
"exception": false,
- "start_time": "2020-03-25T08:24:27.265686",
+ "start_time": "2020-03-26T14:05:22.516194",
"status": "completed"
},
"tags": []
@@ -200,10 +200,10 @@
"source_hidden": true
},
"papermill": {
- "duration": 0.025042,
- "end_time": "2020-03-25T08:24:54.536174",
+ "duration": 0.037168,
+ "end_time": "2020-03-26T14:05:48.685520",
"exception": false,
- "start_time": "2020-03-25T08:24:54.511132",
+ "start_time": "2020-03-26T14:05:48.648352",
"status": "completed"
},
"tags": []
@@ -232,10 +232,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008773,
- "end_time": "2020-03-25T08:24:54.555763",
+ "duration": 0.009516,
+ "end_time": "2020-03-26T14:05:48.711168",
"exception": false,
- "start_time": "2020-03-25T08:24:54.546990",
+ "start_time": "2020-03-26T14:05:48.701652",
"status": "completed"
},
"tags": []
@@ -252,10 +252,10 @@
"source_hidden": true
},
"papermill": {
- "duration": 0.158368,
- "end_time": "2020-03-25T08:24:54.722757",
+ "duration": 0.166126,
+ "end_time": "2020-03-26T14:05:48.884751",
"exception": false,
- "start_time": "2020-03-25T08:24:54.564389",
+ "start_time": "2020-03-26T14:05:48.718625",
"status": "completed"
},
"tags": []
@@ -265,10 +265,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-c0cee81789674bdea2b6db203e3dc151\"></div>\n",
+ "<div id=\"altair-viz-d7b06db3054c463e9825313a25e723f2\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-c0cee81789674bdea2b6db203e3dc151\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-d7b06db3054c463e9825313a25e723f2\");\n",
" const paths = {\n",
" \"vega\": \"https://cdn.jsdelivr.net/npm//vega@5?noext\",\n",
" \"vega-lib\": \"https://cdn.jsdelivr.net/npm//vega-lib?noext\",\n",
@@ -309,7 +309,7 @@
" .catch(showError)\n",
" .then(() => displayChart(vegaEmbed));\n",
" }\n",
- " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}, \"title\": {\"anchor\": \"middle\"}}, \"hconcat\": [{\"mark\": \"line\", \"encoding\": {\"color\": {\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"legend\": {\"title\": \"Canton\"}}, \"opacity\": {\"condition\": {\"value\": 1, \"selection\": \"selector001\"}, \"value\": 0.2}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"title\": \"Canton\"}, {\"type\": \"quantitative\", \"field\": \"ncumul_conf\", \"title\": \"Cases\"}, {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}], \"x\": {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"ncumul_conf\", \"scale\": {\"type\": \"linear\"}, \"title\": \"Cases\"}}, \"selection\": {\"selector001\": {\"type\": \"multi\", \"fields\": [\"abbreviation_canton_and_fl\"], \"bind\": \"legend\"}}}, {\"mark\": \"line\", \"encoding\": {\"color\": {\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"legend\": {\"title\": \"Canton\"}}, \"opacity\": {\"condition\": {\"value\": 1, \"selection\": \"selector002\"}, \"value\": 0.2}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"title\": \"Canton\"}, {\"type\": \"quantitative\", \"field\": \"ncumul_conf_10k\", \"title\": \"Cases/10k\"}, {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}], \"x\": {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"ncumul_conf_10k\", \"scale\": {\"type\": \"linear\"}, \"title\": \"Cases per 10k population\"}}, \"selection\": {\"selector002\": {\"type\": \"multi\", \"fields\": [\"abbreviation_canton_and_fl\"], \"bind\": \"legend\"}}}], \"data\": {\"name\": \"data-d594b3118ac817981f3f304373c2ba11\"}, \"title\": \"Covid-19 cases in Switzerland by Canton\", \"$schema\": 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\"ncumul_deceased\": null, \"source\": \"https://vs.ch/documents/529400/6789273/2020+03+03+-+Medienmitteilung+-+Best%C3%A4tigung+2.+Fall.pdf/9e063e45-70a1-682e-fc37-31d9685f71f1?t=1583233390225\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_10k\": 0.05814714134116382, \"ncumul_deceased_10k\": null}, {\"date\": \"2020-03-05T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 3.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": 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"text/plain": [
@@ -512,16 +512,16 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 29.684337,
- "end_time": "2020-03-25T08:24:55.334159",
+ "duration": 28.669979,
+ "end_time": "2020-03-26T14:05:49.496675",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/mz1u59o4/notebooks/openzh-covid-19-dashboard.ipynb",
+ "input_path": "notebooks/openzh-covid-19-dashboard.ipynb",
"output_path": "runs/openzh-covid-19-dashboard.run.ipynb",
"parameters": {
- "data_path": "/tmp/mz1u59o4/data/openzh-covid-19"
+ "data_path": "data/openzh-covid-19/"
},
- "start_time": "2020-03-25T08:24:25.649822",
+ "start_time": "2020-03-26T14:05:20.826696",
"version": "1.1.0"
}
},
--
GitLab