From 0133586c4c4db42c21320a753a63e6301f0e9b0f Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <cramakri+covid-cron@ethz.ch>
Date: Sun, 22 Mar 2020 08:22:04 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../38fa44222ca5468aa9e5ec5d96608b96.cwl | 120 ++++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 108 ++++++++--------
4 files changed, 178 insertions(+), 58 deletions(-)
create mode 100644 .renku/workflow/38fa44222ca5468aa9e5ec5d96608b96.cwl
diff --git a/.renku/workflow/38fa44222ca5468aa9e5ec5d96608b96.cwl b/.renku/workflow/38fa44222ca5468aa9e5ec5d96608b96.cwl
new file mode 100644
index 00000000..a973614c
--- /dev/null
+++ b/.renku/workflow/38fa44222ca5468aa9e5ec5d96608b96.cwl
@@ -0,0 +1,120 @@
+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_0:
+ outputSource: step_2/output_0
+ streamable: false
+ type: File
+ output_2:
+ outputSource: step_2/output_1
+ streamable: false
+ type: Directory
+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_0
+ - output_1
+ run: ff5f474d38144c5d882c0036bd1059c2_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/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index e1a247a7..70b32619 100644
--- a/data/covidtracking/states-daily.json
+++ b/data/covidtracking/states-daily.json
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:a77694fad0e5a3535a958885f2411ce55bfad90d38d95b908360b69e2914255b
-size 125534
+oid sha256:0c3c20afab79ee8a58c86d9e5e874ece8d14ade025471f38b055ce2fbe9e7a19
+size 134255
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 57cba581..e1e43bbd 100644
--- a/data/covidtracking/states-metadata.json
+++ b/data/covidtracking/states-metadata.json
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:ad39d5a2d631281cda4edbb6b660556bf8ac46a1c12520a9106b53b7d43c9a0c
-size 25673
+oid sha256:7f58c89f6e95859ad0e56742374bd2aa45e76b2e2e13b3a657066459ccd619c4
+size 25781
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 070806c9..6eadb6a6 100644
--- a/runs/download-covidtracking-data.runs.ipynb
+++ b/runs/download-covidtracking-data.runs.ipynb
@@ -5,10 +5,10 @@
"execution_count": 1,
"metadata": {
"papermill": {
- "duration": 3.807963,
- "end_time": "2020-03-21T21:18:07.631574",
+ "duration": 0.527885,
+ "end_time": "2020-03-22T08:22:00.825645",
"exception": false,
- "start_time": "2020-03-21T21:18:03.823611",
+ "start_time": "2020-03-22T08:22:00.297760",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.019935,
- "end_time": "2020-03-21T21:18:07.664678",
+ "duration": 0.016824,
+ "end_time": "2020-03-22T08:22:00.852469",
"exception": false,
- "start_time": "2020-03-21T21:18:07.644743",
+ "start_time": "2020-03-22T08:22:00.835645",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.021741,
- "end_time": "2020-03-21T21:18:07.695982",
+ "duration": 0.018322,
+ "end_time": "2020-03-22T08:22:00.878621",
"exception": false,
- "start_time": "2020-03-21T21:18:07.674241",
+ "start_time": "2020-03-22T08:22:00.860299",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/397wwqxv/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/mhe9_fx8/notebooks/process/download-covidtracking-data.ipynb\"\n",
"PAPERMILL_OUTPUT_PATH = \"runs/download-covidtracking-data.runs.ipynb\"\n",
"out_folder = \"data/covidtracking\"\n"
]
@@ -68,10 +68,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008379,
- "end_time": "2020-03-21T21:18:07.713115",
+ "duration": 0.01311,
+ "end_time": "2020-03-22T08:22:00.900103",
"exception": false,
- "start_time": "2020-03-21T21:18:07.704736",
+ "start_time": "2020-03-22T08:22:00.886993",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.398279,
- "end_time": "2020-03-21T21:18:08.119632",
+ "duration": 1.439286,
+ "end_time": "2020-03-22T08:22:02.347578",
"exception": false,
- "start_time": "2020-03-21T21:18:07.721353",
+ "start_time": "2020-03-22T08:22:00.908292",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.023593,
- "end_time": "2020-03-21T21:18:08.154644",
+ "duration": 0.018345,
+ "end_time": "2020-03-22T08:22:02.374606",
"exception": false,
- "start_time": "2020-03-21T21:18:08.131051",
+ "start_time": "2020-03-22T08:22:02.356261",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.069188,
- "end_time": "2020-03-21T21:18:08.235282",
+ "duration": 0.064418,
+ "end_time": "2020-03-22T08:22:02.448313",
"exception": false,
- "start_time": "2020-03-21T21:18:08.166094",
+ "start_time": "2020-03-22T08:22:02.383895",
"status": "completed"
},
"tags": []
@@ -239,10 +239,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008146,
- "end_time": "2020-03-21T21:18:08.252868",
+ "duration": 0.007933,
+ "end_time": "2020-03-22T08:22:02.465634",
"exception": false,
- "start_time": "2020-03-21T21:18:08.244722",
+ "start_time": "2020-03-22T08:22:02.457701",
"status": "completed"
},
"tags": []
@@ -256,10 +256,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.136609,
- "end_time": "2020-03-21T21:18:08.397510",
+ "duration": 0.840779,
+ "end_time": "2020-03-22T08:22:03.314317",
"exception": false,
- "start_time": "2020-03-21T21:18:08.260901",
+ "start_time": "2020-03-22T08:22:02.473538",
"status": "completed"
},
"tags": []
@@ -276,10 +276,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.023235,
- "end_time": "2020-03-21T21:18:08.431887",
+ "duration": 0.021605,
+ "end_time": "2020-03-22T08:22:03.348671",
"exception": false,
- "start_time": "2020-03-21T21:18:08.408652",
+ "start_time": "2020-03-22T08:22:03.327066",
"status": "completed"
},
"tags": []
@@ -298,10 +298,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.059119,
- "end_time": "2020-03-21T21:18:08.500951",
+ "duration": 0.055687,
+ "end_time": "2020-03-22T08:22:03.415289",
"exception": false,
- "start_time": "2020-03-21T21:18:08.441832",
+ "start_time": "2020-03-22T08:22:03.359602",
"status": "completed"
},
"tags": []
@@ -311,7 +311,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "813 data points\n"
+ "869 data points\n"
]
},
{
@@ -349,27 +349,27 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200320</td>\n",
+ " <td>20200321</td>\n",
" <td>AK</td>\n",
- " <td>12</td>\n",
- " <td>686.0</td>\n",
- " <td>NaN</td>\n",
+ " <td>14.0</td>\n",
+ " <td>758.0</td>\n",
" <td>NaN</td>\n",
+ " <td>0.0</td>\n",
" <td>NaN</td>\n",
- " <td>698</td>\n",
- " <td>2020-03-20T20:00:00Z</td>\n",
+ " <td>772</td>\n",
+ " <td>2020-03-21T20:00:00Z</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200320</td>\n",
+ " <td>20200321</td>\n",
" <td>AL</td>\n",
- " <td>81</td>\n",
+ " <td>124.0</td>\n",
" <td>28.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>0.0</td>\n",
- " <td>109</td>\n",
- " <td>2020-03-20T20:00:00Z</td>\n",
+ " <td>152</td>\n",
+ " <td>2020-03-21T20:00:00Z</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
@@ -377,12 +377,12 @@
],
"text/plain": [
" date state positive negative pending hospitalized death total \\\n",
- "0 20200320 AK 12 686.0 NaN NaN NaN 698 \n",
- "1 20200320 AL 81 28.0 NaN NaN 0.0 109 \n",
+ "0 20200321 AK 14.0 758.0 NaN 0.0 NaN 772 \n",
+ "1 20200321 AL 124.0 28.0 NaN NaN 0.0 152 \n",
"\n",
" dateChecked \n",
- "0 2020-03-20T20:00:00Z \n",
- "1 2020-03-20T20:00:00Z "
+ "0 2020-03-21T20:00:00Z \n",
+ "1 2020-03-21T20:00:00Z "
]
},
"execution_count": 9,
@@ -416,18 +416,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 6.532057,
- "end_time": "2020-03-21T21:18:08.825900",
+ "duration": 4.297689,
+ "end_time": "2020-03-22T08:22:03.739739",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/397wwqxv/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/mhe9_fx8/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/397wwqxv/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/mhe9_fx8/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-03-21T21:18:02.293843",
+ "start_time": "2020-03-22T08:21:59.442050",
"version": "1.1.0"
}
},
--
GitLab