From 56d0346959bd787df1957ac9cfae0967de3d9148 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <cramakri+covid-cron@ethz.ch>
Date: Fri, 20 Mar 2020 21:46:16 +0000
Subject: [PATCH] renku update --with-siblings
---
.../b265ffce7217429599a71f0509a6eb9e.cwl | 125 +++++++++++++
runs/CompileGeoData.run.ipynb | 126 ++++++-------
runs/Dashboard.run.ipynb | 168 +++++++++---------
3 files changed, 272 insertions(+), 147 deletions(-)
create mode 100644 .renku/workflow/b265ffce7217429599a71f0509a6eb9e.cwl
diff --git a/.renku/workflow/b265ffce7217429599a71f0509a6eb9e.cwl b/.renku/workflow/b265ffce7217429599a71f0509a6eb9e.cwl
new file mode 100644
index 00000000..19dbc4f4
--- /dev/null
+++ b/.renku/workflow/b265ffce7217429599a71f0509a6eb9e.cwl
@@ -0,0 +1,125 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: ts_folder
+ streamable: false
+ type: string
+ input_10:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/covid-19_jhu-csse
+ streamable: false
+ type: Directory
+ input_11:
+ default: worldmap_path
+ streamable: false
+ type: string
+ input_12:
+ default:
+ class: File
+ path: ../../data/worldmap/country_centroids.csv
+ streamable: false
+ type: File
+ input_13:
+ default: out_folder
+ streamable: false
+ type: string
+ input_14:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/geodata
+ streamable: false
+ type: Directory
+ input_15:
+ default:
+ class: File
+ path: ../../notebooks/process/CompileGeoData.ipynb
+ streamable: false
+ type: File
+ input_16:
+ default: runs/CompileGeoData.run.ipynb
+ streamable: false
+ type: string
+ input_2:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/covid-19_jhu-csse
+ streamable: false
+ type: Directory
+ input_3:
+ default: rates_folder
+ streamable: false
+ type: string
+ input_4:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/covid-19_rates
+ streamable: false
+ type: Directory
+ input_5:
+ default: geodata_path
+ streamable: false
+ type: string
+ input_6:
+ default:
+ class: File
+ path: ../../data/geodata/geo_data.csv
+ streamable: false
+ type: File
+ input_7:
+ default:
+ class: File
+ path: ../../notebooks/Dashboard.ipynb
+ streamable: false
+ type: File
+ input_8:
+ default: runs/Dashboard.run.ipynb
+ streamable: false
+ type: string
+ input_9:
+ default: ts_folder
+ streamable: false
+ type: string
+outputs:
+ output_0:
+ outputSource: step_1/output_0
+ streamable: false
+ type: File
+ output_1:
+ outputSource: step_2/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
+ input_5: input_5
+ input_6: input_6
+ input_7: input_7
+ input_8: input_8
+ out:
+ - output_0
+ run: 5ae9a9961e194e7795df04a9722452e8_papermill.cwl
+ step_2:
+ in:
+ input_1: input_9
+ input_2: input_10
+ input_3: input_11
+ input_4: input_12
+ input_5: input_13
+ input_6: input_14
+ input_7: input_15
+ input_8: input_16
+ out:
+ - output_0
+ run: a8b2f47629164158a118963ae58eea3b_papermill.cwl
diff --git a/runs/CompileGeoData.run.ipynb b/runs/CompileGeoData.run.ipynb
index e4dacc5f..df4d87d5 100644
--- a/runs/CompileGeoData.run.ipynb
+++ b/runs/CompileGeoData.run.ipynb
@@ -4,10 +4,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.015483,
- "end_time": "2020-03-20T09:14:18.165661",
+ "duration": 0.017678,
+ "end_time": "2020-03-20T21:46:14.724207",
"exception": false,
- "start_time": "2020-03-20T09:14:18.150178",
+ "start_time": "2020-03-20T21:46:14.706529",
"status": "completed"
},
"tags": []
@@ -23,10 +23,10 @@
"execution_count": 1,
"metadata": {
"papermill": {
- "duration": 0.322375,
- "end_time": "2020-03-20T09:14:18.498594",
+ "duration": 0.322985,
+ "end_time": "2020-03-20T21:46:15.058915",
"exception": false,
- "start_time": "2020-03-20T09:14:18.176219",
+ "start_time": "2020-03-20T21:46:14.735930",
"status": "completed"
},
"tags": []
@@ -42,10 +42,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.019323,
- "end_time": "2020-03-20T09:14:18.528885",
+ "duration": 0.019294,
+ "end_time": "2020-03-20T21:46:15.093747",
"exception": false,
- "start_time": "2020-03-20T09:14:18.509562",
+ "start_time": "2020-03-20T21:46:15.074453",
"status": "completed"
},
"tags": []
@@ -62,10 +62,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.009687,
- "end_time": "2020-03-20T09:14:18.548819",
+ "duration": 0.009576,
+ "end_time": "2020-03-20T21:46:15.115538",
"exception": false,
- "start_time": "2020-03-20T09:14:18.539132",
+ "start_time": "2020-03-20T21:46:15.105962",
"status": "completed"
},
"tags": [
@@ -81,10 +81,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.024444,
- "end_time": "2020-03-20T09:14:18.583123",
+ "duration": 0.020198,
+ "end_time": "2020-03-20T21:46:15.145269",
"exception": false,
- "start_time": "2020-03-20T09:14:18.558679",
+ "start_time": "2020-03-20T21:46:15.125071",
"status": "completed"
},
"tags": [
@@ -94,11 +94,11 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/vxmaiyhe/notebooks/process/CompileGeoData.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/n6nbb565/notebooks/process/CompileGeoData.ipynb\"\n",
"PAPERMILL_OUTPUT_PATH = \"runs/CompileGeoData.run.ipynb\"\n",
- "ts_folder = \"/tmp/vxmaiyhe/data/covid-19_jhu-csse\"\n",
- "worldmap_path = \"/tmp/vxmaiyhe/data/worldmap/country_centroids.csv\"\n",
- "out_folder = \"/tmp/vxmaiyhe/data/geodata\"\n"
+ "ts_folder = \"/tmp/n6nbb565/data/covid-19_jhu-csse\"\n",
+ "worldmap_path = \"/tmp/n6nbb565/data/worldmap/country_centroids.csv\"\n",
+ "out_folder = \"/tmp/n6nbb565/data/geodata\"\n"
]
},
{
@@ -106,10 +106,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.031175,
- "end_time": "2020-03-20T09:14:18.627531",
+ "duration": 0.023663,
+ "end_time": "2020-03-20T21:46:15.180074",
"exception": false,
- "start_time": "2020-03-20T09:14:18.596356",
+ "start_time": "2020-03-20T21:46:15.156411",
"status": "completed"
},
"tags": []
@@ -130,10 +130,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.059189,
- "end_time": "2020-03-20T09:14:18.700819",
+ "duration": 0.054183,
+ "end_time": "2020-03-20T21:46:15.246608",
"exception": false,
- "start_time": "2020-03-20T09:14:18.641630",
+ "start_time": "2020-03-20T21:46:15.192425",
"status": "completed"
},
"tags": []
@@ -147,10 +147,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.009298,
- "end_time": "2020-03-20T09:14:18.723004",
+ "duration": 0.010179,
+ "end_time": "2020-03-20T21:46:15.270430",
"exception": false,
- "start_time": "2020-03-20T09:14:18.713706",
+ "start_time": "2020-03-20T21:46:15.260251",
"status": "completed"
},
"tags": []
@@ -164,10 +164,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.04251,
- "end_time": "2020-03-20T09:14:18.775041",
+ "duration": 0.039445,
+ "end_time": "2020-03-20T21:46:15.320605",
"exception": false,
- "start_time": "2020-03-20T09:14:18.732531",
+ "start_time": "2020-03-20T21:46:15.281160",
"status": "completed"
},
"tags": []
@@ -184,10 +184,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.036985,
- "end_time": "2020-03-20T09:14:18.826525",
+ "duration": 0.036049,
+ "end_time": "2020-03-20T21:46:15.370897",
"exception": false,
- "start_time": "2020-03-20T09:14:18.789540",
+ "start_time": "2020-03-20T21:46:15.334848",
"status": "completed"
},
"tags": []
@@ -214,10 +214,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.010156,
- "end_time": "2020-03-20T09:14:18.850018",
+ "duration": 0.010081,
+ "end_time": "2020-03-20T21:46:15.394797",
"exception": false,
- "start_time": "2020-03-20T09:14:18.839862",
+ "start_time": "2020-03-20T21:46:15.384716",
"status": "completed"
},
"tags": []
@@ -231,10 +231,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.025861,
- "end_time": "2020-03-20T09:14:18.886195",
+ "duration": 0.023787,
+ "end_time": "2020-03-20T21:46:15.428815",
"exception": false,
- "start_time": "2020-03-20T09:14:18.860334",
+ "start_time": "2020-03-20T21:46:15.405028",
"status": "completed"
},
"tags": []
@@ -260,10 +260,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.020279,
- "end_time": "2020-03-20T09:14:18.920285",
+ "duration": 0.020553,
+ "end_time": "2020-03-20T21:46:15.463075",
"exception": false,
- "start_time": "2020-03-20T09:14:18.900006",
+ "start_time": "2020-03-20T21:46:15.442522",
"status": "completed"
},
"tags": []
@@ -278,10 +278,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.011006,
- "end_time": "2020-03-20T09:14:18.944832",
+ "duration": 0.011159,
+ "end_time": "2020-03-20T21:46:15.486134",
"exception": false,
- "start_time": "2020-03-20T09:14:18.933826",
+ "start_time": "2020-03-20T21:46:15.474975",
"status": "completed"
},
"tags": []
@@ -295,10 +295,10 @@
"execution_count": 10,
"metadata": {
"papermill": {
- "duration": 0.035258,
- "end_time": "2020-03-20T09:14:18.989997",
+ "duration": 0.046021,
+ "end_time": "2020-03-20T21:46:15.542446",
"exception": false,
- "start_time": "2020-03-20T09:14:18.954739",
+ "start_time": "2020-03-20T21:46:15.496425",
"status": "completed"
},
"tags": []
@@ -413,10 +413,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.010928,
- "end_time": "2020-03-20T09:14:19.015258",
+ "duration": 0.019504,
+ "end_time": "2020-03-20T21:46:15.583707",
"exception": false,
- "start_time": "2020-03-20T09:14:19.004330",
+ "start_time": "2020-03-20T21:46:15.564203",
"status": "completed"
},
"tags": []
@@ -430,10 +430,10 @@
"execution_count": 11,
"metadata": {
"papermill": {
- "duration": 0.030814,
- "end_time": "2020-03-20T09:14:19.057042",
+ "duration": 0.030535,
+ "end_time": "2020-03-20T21:46:15.627081",
"exception": false,
- "start_time": "2020-03-20T09:14:19.026228",
+ "start_time": "2020-03-20T21:46:15.596546",
"status": "completed"
},
"tags": []
@@ -465,20 +465,20 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 2.099246,
- "end_time": "2020-03-20T09:14:19.381722",
+ "duration": 2.076664,
+ "end_time": "2020-03-20T21:46:15.953254",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/vxmaiyhe/notebooks/process/CompileGeoData.ipynb",
+ "input_path": "/tmp/n6nbb565/notebooks/process/CompileGeoData.ipynb",
"output_path": "runs/CompileGeoData.run.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/vxmaiyhe/notebooks/process/CompileGeoData.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/n6nbb565/notebooks/process/CompileGeoData.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/CompileGeoData.run.ipynb",
- "out_folder": "/tmp/vxmaiyhe/data/geodata",
- "ts_folder": "/tmp/vxmaiyhe/data/covid-19_jhu-csse",
- "worldmap_path": "/tmp/vxmaiyhe/data/worldmap/country_centroids.csv"
+ "out_folder": "/tmp/n6nbb565/data/geodata",
+ "ts_folder": "/tmp/n6nbb565/data/covid-19_jhu-csse",
+ "worldmap_path": "/tmp/n6nbb565/data/worldmap/country_centroids.csv"
},
- "start_time": "2020-03-20T09:14:17.282476",
+ "start_time": "2020-03-20T21:46:13.876590",
"version": "1.1.0"
}
},
diff --git a/runs/Dashboard.run.ipynb b/runs/Dashboard.run.ipynb
index 70d3dd06..215bb425 100644
--- a/runs/Dashboard.run.ipynb
+++ b/runs/Dashboard.run.ipynb
@@ -5,10 +5,10 @@
"execution_count": 1,
"metadata": {
"papermill": {
- "duration": 0.553001,
- "end_time": "2020-03-20T09:14:25.719408",
+ "duration": 0.857375,
+ "end_time": "2020-03-20T21:46:09.850069",
"exception": false,
- "start_time": "2020-03-20T09:14:25.166407",
+ "start_time": "2020-03-20T21:46:08.992694",
"status": "completed"
},
"tags": []
@@ -27,10 +27,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.029391,
- "end_time": "2020-03-20T09:14:25.762495",
+ "duration": 0.026586,
+ "end_time": "2020-03-20T21:46:09.892447",
"exception": false,
- "start_time": "2020-03-20T09:14:25.733104",
+ "start_time": "2020-03-20T21:46:09.865861",
"status": "completed"
},
"tags": [
@@ -51,10 +51,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.025671,
- "end_time": "2020-03-20T09:14:25.803507",
+ "duration": 0.025765,
+ "end_time": "2020-03-20T21:46:09.931342",
"exception": false,
- "start_time": "2020-03-20T09:14:25.777836",
+ "start_time": "2020-03-20T21:46:09.905577",
"status": "completed"
},
"tags": [
@@ -64,11 +64,11 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/zeab0m06/notebooks/Dashboard.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/w4fya_83/notebooks/Dashboard.ipynb\"\n",
"PAPERMILL_OUTPUT_PATH = \"runs/Dashboard.run.ipynb\"\n",
- "ts_folder = \"/tmp/zeab0m06/data/covid-19_jhu-csse\"\n",
- "rates_folder = \"/tmp/zeab0m06/data/covid-19_rates\"\n",
- "geodata_path = \"/tmp/zeab0m06/data/geodata/geo_data.csv\"\n"
+ "ts_folder = \"/tmp/w4fya_83/data/covid-19_jhu-csse\"\n",
+ "rates_folder = \"/tmp/w4fya_83/data/covid-19_rates\"\n",
+ "geodata_path = \"/tmp/w4fya_83/data/geodata/geo_data.csv\"\n"
]
},
{
@@ -76,10 +76,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.022861,
- "end_time": "2020-03-20T09:14:25.839629",
+ "duration": 0.023502,
+ "end_time": "2020-03-20T21:46:09.970106",
"exception": false,
- "start_time": "2020-03-20T09:14:25.816768",
+ "start_time": "2020-03-20T21:46:09.946604",
"status": "completed"
},
"tags": []
@@ -94,10 +94,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.149728,
- "end_time": "2020-03-20T09:14:26.002986",
+ "duration": 0.144275,
+ "end_time": "2020-03-20T21:46:10.128936",
"exception": false,
- "start_time": "2020-03-20T09:14:25.853258",
+ "start_time": "2020-03-20T21:46:09.984661",
"status": "completed"
},
"tags": []
@@ -118,10 +118,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.011877,
- "end_time": "2020-03-20T09:14:26.032141",
+ "duration": 0.012758,
+ "end_time": "2020-03-20T21:46:10.157623",
"exception": false,
- "start_time": "2020-03-20T09:14:26.020264",
+ "start_time": "2020-03-20T21:46:10.144865",
"status": "completed"
},
"tags": []
@@ -139,10 +139,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.036872,
- "end_time": "2020-03-20T09:14:26.081115",
+ "duration": 0.035981,
+ "end_time": "2020-03-20T21:46:10.206006",
"exception": false,
- "start_time": "2020-03-20T09:14:26.044243",
+ "start_time": "2020-03-20T21:46:10.170025",
"status": "completed"
},
"tags": []
@@ -170,10 +170,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.013254,
- "end_time": "2020-03-20T09:14:26.111471",
+ "duration": 0.012925,
+ "end_time": "2020-03-20T21:46:10.234679",
"exception": false,
- "start_time": "2020-03-20T09:14:26.098217",
+ "start_time": "2020-03-20T21:46:10.221754",
"status": "completed"
},
"tags": []
@@ -187,10 +187,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.023826,
- "end_time": "2020-03-20T09:14:26.148435",
+ "duration": 0.026402,
+ "end_time": "2020-03-20T21:46:10.276075",
"exception": false,
- "start_time": "2020-03-20T09:14:26.124609",
+ "start_time": "2020-03-20T21:46:10.249673",
"status": "completed"
},
"tags": []
@@ -205,10 +205,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.047914,
- "end_time": "2020-03-20T09:14:26.212529",
+ "duration": 0.051649,
+ "end_time": "2020-03-20T21:46:10.343175",
"exception": false,
- "start_time": "2020-03-20T09:14:26.164615",
+ "start_time": "2020-03-20T21:46:10.291526",
"status": "completed"
},
"tags": []
@@ -223,10 +223,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.138699,
- "end_time": "2020-03-20T09:14:26.366211",
+ "duration": 0.145342,
+ "end_time": "2020-03-20T21:46:10.505195",
"exception": false,
- "start_time": "2020-03-20T09:14:26.227512",
+ "start_time": "2020-03-20T21:46:10.359853",
"status": "completed"
},
"tags": []
@@ -236,10 +236,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-707539e0d9894b98bb4e6f79e36a3dd3\"></div>\n",
+ "<div id=\"altair-viz-3f8b781da7f54aeb93dfbd69c1442017\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-707539e0d9894b98bb4e6f79e36a3dd3\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-3f8b781da7f54aeb93dfbd69c1442017\");\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",
@@ -323,10 +323,10 @@
"execution_count": 10,
"metadata": {
"papermill": {
- "duration": 0.109091,
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- "input_path": "/tmp/zeab0m06/notebooks/Dashboard.ipynb",
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"parameters": {
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- "rates_folder": "/tmp/zeab0m06/data/covid-19_rates",
- "ts_folder": "/tmp/zeab0m06/data/covid-19_jhu-csse"
+ "geodata_path": "/tmp/w4fya_83/data/geodata/geo_data.csv",
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+ "ts_folder": "/tmp/w4fya_83/data/covid-19_jhu-csse"
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+ "start_time": "2020-03-20T21:46:07.889883",
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--
GitLab