From 87fd65d0e2985a18905e252137ce772ad2ecdbf8 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <cramakri+covid-cron@ethz.ch>
Date: Tue, 14 Apr 2020 07:25:23 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../b841533a5b4940f0b591cfa704e86674.cwl | 148 +++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 150 +++++++++---------
4 files changed, 227 insertions(+), 79 deletions(-)
create mode 100644 .renku/workflow/b841533a5b4940f0b591cfa704e86674.cwl
diff --git a/.renku/workflow/b841533a5b4940f0b591cfa704e86674.cwl b/.renku/workflow/b841533a5b4940f0b591cfa704e86674.cwl
new file mode 100644
index 000000000..b04828698
--- /dev/null
+++ b/.renku/workflow/b841533a5b4940f0b591cfa704e86674.cwl
@@ -0,0 +1,148 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: out_folder
+ streamable: false
+ type: string
+ input_10:
+ default: states-metadata.json
+ streamable: false
+ type: string
+ input_2:
+ default: data/covidtracking
+ streamable: false
+ type: string
+ input_3:
+ default:
+ class: File
+ path: ../../notebooks/process/download-covidtracking-data.ipynb
+ streamable: false
+ type: File
+ input_4:
+ default: runs/download-covidtracking-data.runs.ipynb
+ streamable: false
+ type: string
+ input_5:
+ default: out_folder
+ streamable: false
+ type: string
+ input_6:
+ default: data/covidtracking
+ streamable: false
+ type: string
+ input_7:
+ default:
+ class: File
+ path: ../../notebooks/process/download-covidtracking-data.ipynb
+ streamable: false
+ type: File
+ input_8:
+ default: runs/download-covidtracking-data.runs.ipynb
+ streamable: false
+ type: string
+ input_9:
+ default: states-daily.json
+ streamable: false
+ type: string
+outputs:
+ output_0:
+ outputSource: step_1/output_0
+ streamable: false
+ type: File
+ output_3:
+ outputSource: step_1/output_1
+ streamable: false
+ type: Directory
+requirements: []
+steps:
+ step_1:
+ in:
+ input_1: input_1
+ input_2: input_2
+ input_3: input_3
+ input_4: input_4
+ out:
+ - output_0
+ - output_1
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
+ step_2:
+ in:
+ input_1: input_5
+ input_2: input_6
+ input_3: input_7
+ input_4: input_8
+ out:
+ - output_0
+ - output_1
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
+ step_3:
+ in:
+ filename: input_9
+ 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_4:
+ in:
+ filename: input_10
+ input_directory: step_1/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 5121d0016..170e3e5d2 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:ea956c215a6571a4dacec07b3dbd77d9e37b5aeb360b0765e1637dd7202d6d97
-size 1014851
+oid sha256:ec936832d654871aa4d6683c980863415ca4815d42c5ae515389279bbfec19d6
+size 1045984
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 96cd905db..460f365c0 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 sha256:4815f2cceb7c2c32731794ab5b04dd129ea7f7ad3df2b54b0295d3eb55f1f767
-size 27071
+oid sha256:45eedd74dfc95f1330400740f8e25ce63adfcaef3082729afa9d76cb284a869b
+size 27113
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index c557160dd..0ae908d0a 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": 3.890284,
- "end_time": "2020-04-13T07:24:35.128446",
+ "duration": 2.928723,
+ "end_time": "2020-04-14T07:25:18.173122",
"exception": false,
- "start_time": "2020-04-13T07:24:31.238162",
+ "start_time": "2020-04-14T07:25:15.244399",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.024841,
- "end_time": "2020-04-13T07:24:35.168873",
+ "duration": 0.025148,
+ "end_time": "2020-04-14T07:25:18.213431",
"exception": false,
- "start_time": "2020-04-13T07:24:35.144032",
+ "start_time": "2020-04-14T07:25:18.188283",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.024245,
- "end_time": "2020-04-13T07:24:35.201283",
+ "duration": 0.021431,
+ "end_time": "2020-04-14T07:25:18.244432",
"exception": false,
- "start_time": "2020-04-13T07:24:35.177038",
+ "start_time": "2020-04-14T07:25:18.223001",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/1yrezeoo/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/y5i25jab/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": 0.007503,
- "end_time": "2020-04-13T07:24:35.217583",
+ "duration": 0.005677,
+ "end_time": "2020-04-14T07:25:18.257346",
"exception": false,
- "start_time": "2020-04-13T07:24:35.210080",
+ "start_time": "2020-04-14T07:25:18.251669",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.191268,
- "end_time": "2020-04-13T07:24:35.414542",
+ "duration": 0.601563,
+ "end_time": "2020-04-14T07:25:18.864512",
"exception": false,
- "start_time": "2020-04-13T07:24:35.223274",
+ "start_time": "2020-04-14T07:25:18.262949",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.026264,
- "end_time": "2020-04-13T07:24:35.456863",
+ "duration": 0.027589,
+ "end_time": "2020-04-14T07:25:18.907156",
"exception": false,
- "start_time": "2020-04-13T07:24:35.430599",
+ "start_time": "2020-04-14T07:25:18.879567",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.072516,
- "end_time": "2020-04-13T07:24:35.542366",
+ "duration": 0.076892,
+ "end_time": "2020-04-14T07:25:18.996665",
"exception": false,
- "start_time": "2020-04-13T07:24:35.469850",
+ "start_time": "2020-04-14T07:25:18.919773",
"status": "completed"
},
"tags": []
@@ -246,10 +246,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008042,
- "end_time": "2020-04-13T07:24:35.563359",
+ "duration": 0.008701,
+ "end_time": "2020-04-14T07:25:19.019188",
"exception": false,
- "start_time": "2020-04-13T07:24:35.555317",
+ "start_time": "2020-04-14T07:25:19.010487",
"status": "completed"
},
"tags": []
@@ -263,10 +263,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.214373,
- "end_time": "2020-04-13T07:24:35.784160",
+ "duration": 0.331311,
+ "end_time": "2020-04-14T07:25:19.357567",
"exception": false,
- "start_time": "2020-04-13T07:24:35.569787",
+ "start_time": "2020-04-14T07:25:19.026256",
"status": "completed"
},
"tags": []
@@ -283,10 +283,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.028526,
- "end_time": "2020-04-13T07:24:35.827965",
+ "duration": 0.03064,
+ "end_time": "2020-04-14T07:25:19.402444",
"exception": false,
- "start_time": "2020-04-13T07:24:35.799439",
+ "start_time": "2020-04-14T07:25:19.371804",
"status": "completed"
},
"tags": []
@@ -305,10 +305,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.105363,
- "end_time": "2020-04-13T07:24:35.945309",
+ "duration": 0.107173,
+ "end_time": "2020-04-14T07:25:19.520920",
"exception": false,
- "start_time": "2020-04-13T07:24:35.839946",
+ "start_time": "2020-04-14T07:25:19.413747",
"status": "completed"
},
"tags": []
@@ -318,7 +318,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "2112 data points\n"
+ "2168 data points\n"
]
},
{
@@ -368,51 +368,51 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200412</td>\n",
+ " <td>20200413</td>\n",
" <td>AK</td>\n",
- " <td>272.0</td>\n",
- " <td>7766.0</td>\n",
+ " <td>277.0</td>\n",
+ " <td>7553.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>31.0</td>\n",
+ " <td>32.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>31.0</td>\n",
- " <td>8038.0</td>\n",
- " <td>8038.0</td>\n",
- " <td>8038.0</td>\n",
+ " <td>32.0</td>\n",
+ " <td>7830.0</td>\n",
+ " <td>7830.0</td>\n",
+ " <td>7830.0</td>\n",
" <td>2</td>\n",
" <td>0.0</td>\n",
- " <td>0.0</td>\n",
- " <td>291.0</td>\n",
- " <td>15.0</td>\n",
- " <td>306.0</td>\n",
+ " <td>1.0</td>\n",
+ " <td>-213.0</td>\n",
+ " <td>5.0</td>\n",
+ " <td>-208.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200412</td>\n",
+ " <td>20200413</td>\n",
" <td>AL</td>\n",
- " <td>3525.0</td>\n",
- " <td>18058.0</td>\n",
+ " <td>3734.0</td>\n",
+ " <td>25448.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>437.0</td>\n",
+ " <td>457.0</td>\n",
" <td>NaN</td>\n",
" <td>189.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>437.0</td>\n",
- " <td>21583.0</td>\n",
- " <td>21583.0</td>\n",
- " <td>21583.0</td>\n",
+ " <td>457.0</td>\n",
+ " <td>29182.0</td>\n",
+ " <td>29182.0</td>\n",
+ " <td>29182.0</td>\n",
" <td>1</td>\n",
- " <td>2.0</td>\n",
- " <td>35.0</td>\n",
- " <td>0.0</td>\n",
- " <td>334.0</td>\n",
- " <td>334.0</td>\n",
+ " <td>6.0</td>\n",
+ " <td>20.0</td>\n",
+ " <td>7390.0</td>\n",
+ " <td>209.0</td>\n",
+ " <td>7599.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
@@ -421,24 +421,24 @@
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200412 AK 272.0 7766.0 NaN NaN \n",
- "1 20200412 AL 3525.0 18058.0 NaN NaN \n",
+ "0 20200413 AK 277.0 7553.0 NaN NaN \n",
+ "1 20200413 AL 3734.0 25448.0 NaN NaN \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
- "0 31.0 NaN NaN \n",
- "1 437.0 NaN 189.0 \n",
+ "0 32.0 NaN NaN \n",
+ "1 457.0 NaN 189.0 \n",
"\n",
" onVentilatorCurrently ... hospitalized total totalTestResults \\\n",
- "0 NaN ... 31.0 8038.0 8038.0 \n",
- "1 NaN ... 437.0 21583.0 21583.0 \n",
+ "0 NaN ... 32.0 7830.0 7830.0 \n",
+ "1 NaN ... 457.0 29182.0 29182.0 \n",
"\n",
" posNeg fips deathIncrease hospitalizedIncrease negativeIncrease \\\n",
- "0 8038.0 2 0.0 0.0 291.0 \n",
- "1 21583.0 1 2.0 35.0 0.0 \n",
+ "0 7830.0 2 0.0 1.0 -213.0 \n",
+ "1 29182.0 1 6.0 20.0 7390.0 \n",
"\n",
" positiveIncrease totalTestResultsIncrease \n",
- "0 15.0 306.0 \n",
- "1 334.0 334.0 \n",
+ "0 5.0 -208.0 \n",
+ "1 209.0 7599.0 \n",
"\n",
"[2 rows x 25 columns]"
]
@@ -474,18 +474,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 6.078507,
- "end_time": "2020-04-13T07:24:36.274997",
+ "duration": 6.524857,
+ "end_time": "2020-04-14T07:25:19.946947",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/1yrezeoo/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/y5i25jab/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/1yrezeoo/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/y5i25jab/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-04-13T07:24:30.196490",
+ "start_time": "2020-04-14T07:25:13.422090",
"version": "1.1.0"
}
},
--
GitLab