From 2281ce1f8db24e15dbd4e7264d2be4262bbb22f9 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <cramakri+covid-cron@ethz.ch>
Date: Sat, 21 Mar 2020 21:18:56 +0000
Subject: [PATCH] renku update --with-siblings
---
.../c6451b62ed1d4880a03a96ac9f84ecaa.cwl | 66 +++++++
runs/Dashboard.run.ipynb | 168 +++++++++---------
2 files changed, 150 insertions(+), 84 deletions(-)
create mode 100644 .renku/workflow/c6451b62ed1d4880a03a96ac9f84ecaa.cwl
diff --git a/.renku/workflow/c6451b62ed1d4880a03a96ac9f84ecaa.cwl b/.renku/workflow/c6451b62ed1d4880a03a96ac9f84ecaa.cwl
new file mode 100644
index 0000000..635f377
--- /dev/null
+++ b/.renku/workflow/c6451b62ed1d4880a03a96ac9f84ecaa.cwl
@@ -0,0 +1,66 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: ts_folder
+ 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
+outputs:
+ output_0:
+ 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
+ input_5: input_5
+ input_6: input_6
+ input_7: input_7
+ input_8: input_8
+ out:
+ - output_0
+ run: 5ae9a9961e194e7795df04a9722452e8_papermill.cwl
diff --git a/runs/Dashboard.run.ipynb b/runs/Dashboard.run.ipynb
index 5232113..eff9aa9 100644
--- a/runs/Dashboard.run.ipynb
+++ b/runs/Dashboard.run.ipynb
@@ -5,10 +5,10 @@
"execution_count": 1,
"metadata": {
"papermill": {
- "duration": 0.609203,
- "end_time": "2020-03-21T08:21:34.856967",
+ "duration": 1.153935,
+ "end_time": "2020-03-21T21:18:52.710998",
"exception": false,
- "start_time": "2020-03-21T08:21:34.247764",
+ "start_time": "2020-03-21T21:18:51.557063",
"status": "completed"
},
"tags": []
@@ -27,10 +27,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.022235,
- "end_time": "2020-03-21T08:21:34.894425",
+ "duration": 0.024622,
+ "end_time": "2020-03-21T21:18:52.750605",
"exception": false,
- "start_time": "2020-03-21T08:21:34.872190",
+ "start_time": "2020-03-21T21:18:52.725983",
"status": "completed"
},
"tags": [
@@ -51,10 +51,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.022115,
- "end_time": "2020-03-21T08:21:34.927671",
+ "duration": 0.027134,
+ "end_time": "2020-03-21T21:18:52.794529",
"exception": false,
- "start_time": "2020-03-21T08:21:34.905556",
+ "start_time": "2020-03-21T21:18:52.767395",
"status": "completed"
},
"tags": [
@@ -64,11 +64,11 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/t7uqe0kc/notebooks/Dashboard.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/aphx1zdn/notebooks/Dashboard.ipynb\"\n",
"PAPERMILL_OUTPUT_PATH = \"runs/Dashboard.run.ipynb\"\n",
- "ts_folder = \"/tmp/t7uqe0kc/data/covid-19_jhu-csse\"\n",
- "rates_folder = \"/tmp/t7uqe0kc/data/covid-19_rates\"\n",
- "geodata_path = \"/tmp/t7uqe0kc/data/geodata/geo_data.csv\"\n"
+ "ts_folder = \"/tmp/aphx1zdn/data/covid-19_jhu-csse\"\n",
+ "rates_folder = \"/tmp/aphx1zdn/data/covid-19_rates\"\n",
+ "geodata_path = \"/tmp/aphx1zdn/data/geodata/geo_data.csv\"\n"
]
},
{
@@ -76,10 +76,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.023145,
- "end_time": "2020-03-21T08:21:34.964505",
+ "duration": 0.022301,
+ "end_time": "2020-03-21T21:18:52.833918",
"exception": false,
- "start_time": "2020-03-21T08:21:34.941360",
+ "start_time": "2020-03-21T21:18:52.811617",
"status": "completed"
},
"tags": []
@@ -94,10 +94,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.267358,
- "end_time": "2020-03-21T08:21:35.246180",
+ "duration": 0.139378,
+ "end_time": "2020-03-21T21:18:52.986117",
"exception": false,
- "start_time": "2020-03-21T08:21:34.978822",
+ "start_time": "2020-03-21T21:18:52.846739",
"status": "completed"
},
"tags": []
@@ -118,10 +118,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.012804,
- "end_time": "2020-03-21T08:21:35.273057",
+ "duration": 0.01217,
+ "end_time": "2020-03-21T21:18:53.014734",
"exception": false,
- "start_time": "2020-03-21T08:21:35.260253",
+ "start_time": "2020-03-21T21:18:53.002564",
"status": "completed"
},
"tags": []
@@ -139,10 +139,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.035757,
- "end_time": "2020-03-21T08:21:35.321446",
+ "duration": 0.040114,
+ "end_time": "2020-03-21T21:18:53.067652",
"exception": false,
- "start_time": "2020-03-21T08:21:35.285689",
+ "start_time": "2020-03-21T21:18:53.027538",
"status": "completed"
},
"tags": []
@@ -170,10 +170,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.012885,
- "end_time": "2020-03-21T08:21:35.350882",
+ "duration": 0.012791,
+ "end_time": "2020-03-21T21:18:53.097800",
"exception": false,
- "start_time": "2020-03-21T08:21:35.337997",
+ "start_time": "2020-03-21T21:18:53.085009",
"status": "completed"
},
"tags": []
@@ -187,10 +187,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.023769,
- "end_time": "2020-03-21T08:21:35.387608",
+ "duration": 0.025463,
+ "end_time": "2020-03-21T21:18:53.136280",
"exception": false,
- "start_time": "2020-03-21T08:21:35.363839",
+ "start_time": "2020-03-21T21:18:53.110817",
"status": "completed"
},
"tags": []
@@ -205,10 +205,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.05008,
- "end_time": "2020-03-21T08:21:35.451869",
+ "duration": 0.051426,
+ "end_time": "2020-03-21T21:18:53.203059",
"exception": false,
- "start_time": "2020-03-21T08:21:35.401789",
+ "start_time": "2020-03-21T21:18:53.151633",
"status": "completed"
},
"tags": []
@@ -223,10 +223,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.131073,
- "end_time": "2020-03-21T08:21:35.596614",
+ "duration": 0.133784,
+ "end_time": "2020-03-21T21:18:53.354599",
"exception": false,
- "start_time": "2020-03-21T08:21:35.465541",
+ "start_time": "2020-03-21T21:18:53.220815",
"status": "completed"
},
"tags": []
@@ -236,10 +236,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-41e64d099e4d4eeba58793013e400089\"></div>\n",
+ "<div id=\"altair-viz-ce5ac20e01d54114989b6f551e33b7bf\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-41e64d099e4d4eeba58793013e400089\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-ce5ac20e01d54114989b6f551e33b7bf\");\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": 0.121229,
- "end_time": "2020-03-21T08:21:35.733198",
+ "duration": 0.099022,
+ "end_time": "2020-03-21T21:18:53.468182",
"exception": false,
- "start_time": "2020-03-21T08:21:35.611969",
+ "start_time": "2020-03-21T21:18:53.369160",
"status": "completed"
},
"tags": []
@@ -336,10 +336,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-1ee73cb55d3a4a61aed54cbd6a511d94\"></div>\n",
+ "<div id=\"altair-viz-28cc5b4c78c24845a5b66feed87deeb3\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-1ee73cb55d3a4a61aed54cbd6a511d94\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-28cc5b4c78c24845a5b66feed87deeb3\");\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",
@@ -439,10 +439,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.016329,
- "end_time": "2020-03-21T08:21:35.766114",
+ "duration": 0.015934,
+ "end_time": "2020-03-21T21:18:53.500781",
"exception": false,
- "start_time": "2020-03-21T08:21:35.749785",
+ "start_time": "2020-03-21T21:18:53.484847",
"status": "completed"
},
"tags": []
@@ -456,10 +456,10 @@
"execution_count": 11,
"metadata": {
"papermill": {
- "duration": 0.085944,
- "end_time": "2020-03-21T08:21:35.868183",
+ "duration": 0.065121,
+ "end_time": "2020-03-21T21:18:53.581973",
"exception": false,
- "start_time": "2020-03-21T08:21:35.782239",
+ "start_time": "2020-03-21T21:18:53.516852",
"status": "completed"
},
"tags": []
@@ -478,10 +478,10 @@
"execution_count": 12,
"metadata": {
"papermill": {
- "duration": 0.167666,
- "end_time": "2020-03-21T08:21:36.055819",
+ "duration": 0.174955,
+ "end_time": "2020-03-21T21:18:53.773576",
"exception": false,
- "start_time": "2020-03-21T08:21:35.888153",
+ "start_time": "2020-03-21T21:18:53.598621",
"status": "completed"
},
"tags": []
@@ -491,10 +491,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-d35a7707f871457484f71238619832d4\"></div>\n",
+ "<div id=\"altair-viz-20ff26d960284ff4b6e4e893665dd0c2\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-d35a7707f871457484f71238619832d4\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-20ff26d960284ff4b6e4e893665dd0c2\");\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",
@@ -588,10 +588,10 @@
"execution_count": 13,
"metadata": {
"papermill": {
- "duration": 0.365646,
- "end_time": "2020-03-21T08:21:36.447346",
+ "duration": 0.342862,
+ "end_time": "2020-03-21T21:18:54.142920",
"exception": false,
- "start_time": "2020-03-21T08:21:36.081700",
+ "start_time": "2020-03-21T21:18:53.800058",
"status": "completed"
},
"tags": []
@@ -622,10 +622,10 @@
"execution_count": 14,
"metadata": {
"papermill": {
- "duration": 0.046133,
- "end_time": "2020-03-21T08:21:36.524965",
+ "duration": 0.039345,
+ "end_time": "2020-03-21T21:18:54.206365",
"exception": false,
- "start_time": "2020-03-21T08:21:36.478832",
+ "start_time": "2020-03-21T21:18:54.167020",
"status": "completed"
},
"tags": []
@@ -677,10 +677,10 @@
"execution_count": 15,
"metadata": {
"papermill": {
- "duration": 0.381155,
- "end_time": "2020-03-21T08:21:36.935070",
+ "duration": 0.333452,
+ "end_time": "2020-03-21T21:18:54.564887",
"exception": false,
- "start_time": "2020-03-21T08:21:36.553915",
+ "start_time": "2020-03-21T21:18:54.231435",
"status": "completed"
},
"tags": []
@@ -690,10 +690,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-759454c2bc714c72a9efb1b63c824f68\"></div>\n",
+ "<div id=\"altair-viz-91449ad96b024a11b0a8b302f00f81b4\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-759454c2bc714c72a9efb1b63c824f68\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-91449ad96b024a11b0a8b302f00f81b4\");\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",
@@ -789,10 +789,10 @@
"execution_count": 16,
"metadata": {
"papermill": {
- "duration": 0.350725,
- "end_time": "2020-03-21T08:21:37.316238",
+ "duration": 0.356685,
+ "end_time": "2020-03-21T21:18:54.949980",
"exception": false,
- "start_time": "2020-03-21T08:21:36.965513",
+ "start_time": "2020-03-21T21:18:54.593295",
"status": "completed"
},
"tags": []
@@ -802,10 +802,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-6cc2cf9655124091814e613b2c98a8b9\"></div>\n",
+ "<div id=\"altair-viz-a62dc68c257d48c98d06b81c7d5afadb\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-6cc2cf9655124091814e613b2c98a8b9\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-a62dc68c257d48c98d06b81c7d5afadb\");\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",
@@ -897,10 +897,10 @@
"execution_count": 17,
"metadata": {
"papermill": {
- "duration": 0.388646,
- "end_time": "2020-03-21T08:21:37.736333",
+ "duration": 0.357712,
+ "end_time": "2020-03-21T21:18:55.339613",
"exception": false,
- "start_time": "2020-03-21T08:21:37.347687",
+ "start_time": "2020-03-21T21:18:54.981901",
"status": "completed"
},
"tags": []
@@ -910,10 +910,10 @@
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-e69dfa2762804a7b846b16fe8366b26d\"></div>\n",
+ "<div id=\"altair-viz-89efaf09e0ac4886813f72b72801b324\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-e69dfa2762804a7b846b16fe8366b26d\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-89efaf09e0ac4886813f72b72801b324\");\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",
@@ -1022,20 +1022,20 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 4.685241,
- "end_time": "2020-03-21T08:21:38.081354",
+ "duration": 4.975001,
+ "end_time": "2020-03-21T21:18:55.693413",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/t7uqe0kc/notebooks/Dashboard.ipynb",
+ "input_path": "/tmp/aphx1zdn/notebooks/Dashboard.ipynb",
"output_path": "runs/Dashboard.run.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/t7uqe0kc/notebooks/Dashboard.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/aphx1zdn/notebooks/Dashboard.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/Dashboard.run.ipynb",
- "geodata_path": "/tmp/t7uqe0kc/data/geodata/geo_data.csv",
- "rates_folder": "/tmp/t7uqe0kc/data/covid-19_rates",
- "ts_folder": "/tmp/t7uqe0kc/data/covid-19_jhu-csse"
+ "geodata_path": "/tmp/aphx1zdn/data/geodata/geo_data.csv",
+ "rates_folder": "/tmp/aphx1zdn/data/covid-19_rates",
+ "ts_folder": "/tmp/aphx1zdn/data/covid-19_jhu-csse"
},
- "start_time": "2020-03-21T08:21:33.396113",
+ "start_time": "2020-03-21T21:18:50.718412",
"version": "1.1.0"
}
},
--
GitLab