From eba5afe84714da575d74cf8be4ca0fd510f40170 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <cramakri+covid-cron@ethz.ch>
Date: Thu, 9 Apr 2020 07:23:36 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../3dce08156fa1452185ecdbfe7686706d.cwl | 120 ++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 152 +++++++++---------
4 files changed, 200 insertions(+), 80 deletions(-)
create mode 100644 .renku/workflow/3dce08156fa1452185ecdbfe7686706d.cwl
diff --git a/.renku/workflow/3dce08156fa1452185ecdbfe7686706d.cwl b/.renku/workflow/3dce08156fa1452185ecdbfe7686706d.cwl
new file mode 100644
index 000000000..718e884d1
--- /dev/null
+++ b/.renku/workflow/3dce08156fa1452185ecdbfe7686706d.cwl
@@ -0,0 +1,120 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: states-metadata.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-daily.json
+ streamable: false
+ type: string
+outputs:
+ output_0:
+ outputSource: step_2/output_0
+ streamable: false
+ type: File
+ output_3:
+ 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-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_2:
+ in:
+ input_1: input_2
+ input_2: input_3
+ input_3: input_4
+ input_4: input_5
+ out:
+ - output_0
+ - output_1
+ run: a17d560c41a54f5aa307ce5f3c5effe5_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-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/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index 2b98b1f89..477b54e1d 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 sha256:624c4e90483859c5b4f066d76e10a91f79f14c02fb2d5a11ea660e6a3c2e5e4f
-size 856825
+oid sha256:5e87f93ee9862eb047539a22da2e3e6556a9bfa833b0752eb374ea4e492e9416
+size 887669
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 8388329e0..35bc6258d 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:deca95d58f3cb059c7023d28cba9da0d67c1a59bf2e5aa9403bbe32d5e8cfaac
-size 25520
+oid sha256:c64df10b6938f71ba5b9a6a8a7ace894a1c39490db19da83197867961e1796b2
+size 25883
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index aa9bc6674..88ceef3b8 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": 4.461396,
- "end_time": "2020-04-08T07:24:35.331262",
+ "duration": 4.202528,
+ "end_time": "2020-04-09T07:23:34.956443",
"exception": false,
- "start_time": "2020-04-08T07:24:30.869866",
+ "start_time": "2020-04-09T07:23:30.753915",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.026627,
- "end_time": "2020-04-08T07:24:35.373890",
+ "duration": 0.017913,
+ "end_time": "2020-04-09T07:23:34.987901",
"exception": false,
- "start_time": "2020-04-08T07:24:35.347263",
+ "start_time": "2020-04-09T07:23:34.969988",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.027542,
- "end_time": "2020-04-08T07:24:35.414725",
+ "duration": 0.019593,
+ "end_time": "2020-04-09T07:23:35.014482",
"exception": false,
- "start_time": "2020-04-08T07:24:35.387183",
+ "start_time": "2020-04-09T07:23:34.994889",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/e17s3uzn/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/hlryh8jc/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": 0.009615,
- "end_time": "2020-04-08T07:24:35.443594",
+ "duration": 0.006856,
+ "end_time": "2020-04-09T07:23:35.031803",
"exception": false,
- "start_time": "2020-04-08T07:24:35.433979",
+ "start_time": "2020-04-09T07:23:35.024947",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.496555,
- "end_time": "2020-04-08T07:24:35.946501",
+ "duration": 0.170755,
+ "end_time": "2020-04-09T07:23:35.209942",
"exception": false,
- "start_time": "2020-04-08T07:24:35.449946",
+ "start_time": "2020-04-09T07:23:35.039187",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.026674,
- "end_time": "2020-04-08T07:24:35.986611",
+ "duration": 0.02125,
+ "end_time": "2020-04-09T07:23:35.245223",
"exception": false,
- "start_time": "2020-04-08T07:24:35.959937",
+ "start_time": "2020-04-09T07:23:35.223973",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.076069,
- "end_time": "2020-04-08T07:24:36.071390",
+ "duration": 0.065282,
+ "end_time": "2020-04-09T07:23:35.319713",
"exception": false,
- "start_time": "2020-04-08T07:24:35.995321",
+ "start_time": "2020-04-09T07:23:35.254431",
"status": "completed"
},
"tags": []
@@ -246,10 +246,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008016,
- "end_time": "2020-04-08T07:24:36.093347",
+ "duration": 0.008302,
+ "end_time": "2020-04-09T07:23:35.337790",
"exception": false,
- "start_time": "2020-04-08T07:24:36.085331",
+ "start_time": "2020-04-09T07:23:35.329488",
"status": "completed"
},
"tags": []
@@ -263,10 +263,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.289201,
- "end_time": "2020-04-08T07:24:36.389295",
+ "duration": 0.189186,
+ "end_time": "2020-04-09T07:23:35.534942",
"exception": false,
- "start_time": "2020-04-08T07:24:36.100094",
+ "start_time": "2020-04-09T07:23:35.345756",
"status": "completed"
},
"tags": []
@@ -283,10 +283,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.027866,
- "end_time": "2020-04-08T07:24:36.431887",
+ "duration": 0.027995,
+ "end_time": "2020-04-09T07:23:35.573749",
"exception": false,
- "start_time": "2020-04-08T07:24:36.404021",
+ "start_time": "2020-04-09T07:23:35.545754",
"status": "completed"
},
"tags": []
@@ -305,10 +305,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.099568,
- "end_time": "2020-04-08T07:24:36.541506",
+ "duration": 0.105936,
+ "end_time": "2020-04-09T07:23:35.690696",
"exception": false,
- "start_time": "2020-04-08T07:24:36.441938",
+ "start_time": "2020-04-09T07:23:35.584760",
"status": "completed"
},
"tags": []
@@ -318,7 +318,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "1821 data points\n"
+ "1877 data points\n"
]
},
{
@@ -368,51 +368,51 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200407</td>\n",
+ " <td>20200408</td>\n",
" <td>AK</td>\n",
- " <td>213.0</td>\n",
- " <td>6700.0</td>\n",
+ " <td>226.0</td>\n",
+ " <td>6842.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>23.0</td>\n",
+ " <td>27.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>23.0</td>\n",
- " <td>6913</td>\n",
- " <td>6913</td>\n",
- " <td>6913</td>\n",
+ " <td>27.0</td>\n",
+ " <td>7068</td>\n",
+ " <td>7068</td>\n",
+ " <td>7068</td>\n",
" <td>2</td>\n",
- " <td>0.0</td>\n",
- " <td>0.0</td>\n",
- " <td>8.0</td>\n",
- " <td>22.0</td>\n",
- " <td>30.0</td>\n",
+ " <td>1.0</td>\n",
+ " <td>4.0</td>\n",
+ " <td>142.0</td>\n",
+ " <td>13.0</td>\n",
+ " <td>155.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200407</td>\n",
+ " <td>20200408</td>\n",
" <td>AL</td>\n",
- " <td>2119.0</td>\n",
- " <td>12797.0</td>\n",
+ " <td>2369.0</td>\n",
+ " <td>16753.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>271.0</td>\n",
+ " <td>314.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>271.0</td>\n",
- " <td>14916</td>\n",
- " <td>14916</td>\n",
- " <td>14916</td>\n",
+ " <td>314.0</td>\n",
+ " <td>19122</td>\n",
+ " <td>19122</td>\n",
+ " <td>19122</td>\n",
" <td>1</td>\n",
- " <td>6.0</td>\n",
- " <td>31.0</td>\n",
- " <td>0.0</td>\n",
- " <td>151.0</td>\n",
- " <td>151.0</td>\n",
+ " <td>10.0</td>\n",
+ " <td>43.0</td>\n",
+ " <td>3956.0</td>\n",
+ " <td>250.0</td>\n",
+ " <td>4206.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
@@ -421,24 +421,24 @@
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200407 AK 213.0 6700.0 NaN NaN \n",
- "1 20200407 AL 2119.0 12797.0 NaN NaN \n",
+ "0 20200408 AK 226.0 6842.0 NaN NaN \n",
+ "1 20200408 AL 2369.0 16753.0 NaN NaN \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
- "0 23.0 NaN NaN \n",
- "1 271.0 NaN NaN \n",
+ "0 27.0 NaN NaN \n",
+ "1 314.0 NaN NaN \n",
"\n",
" onVentilatorCurrently ... hospitalized total totalTestResults posNeg \\\n",
- "0 NaN ... 23.0 6913 6913 6913 \n",
- "1 NaN ... 271.0 14916 14916 14916 \n",
+ "0 NaN ... 27.0 7068 7068 7068 \n",
+ "1 NaN ... 314.0 19122 19122 19122 \n",
"\n",
" fips deathIncrease hospitalizedIncrease negativeIncrease \\\n",
- "0 2 0.0 0.0 8.0 \n",
- "1 1 6.0 31.0 0.0 \n",
+ "0 2 1.0 4.0 142.0 \n",
+ "1 1 10.0 43.0 3956.0 \n",
"\n",
" positiveIncrease totalTestResultsIncrease \n",
- "0 22.0 30.0 \n",
- "1 151.0 151.0 \n",
+ "0 13.0 155.0 \n",
+ "1 250.0 4206.0 \n",
"\n",
"[2 rows x 25 columns]"
]
@@ -474,18 +474,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 8.231266,
- "end_time": "2020-04-08T07:24:36.871358",
+ "duration": 6.894233,
+ "end_time": "2020-04-09T07:23:36.011265",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/e17s3uzn/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/hlryh8jc/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/e17s3uzn/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/hlryh8jc/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-04-08T07:24:28.640092",
+ "start_time": "2020-04-09T07:23:29.117032",
"version": "1.1.0"
}
},
--
GitLab