From d4aa55c20be17efef631377270cbc23943f75843 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Sat, 7 Nov 2020 07:36:29 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../4b986549374544639a21ec2269579141.cwl | 120 ++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 132 +++++++++---------
4 files changed, 190 insertions(+), 70 deletions(-)
create mode 100644 .renku/workflow/4b986549374544639a21ec2269579141.cwl
diff --git a/.renku/workflow/4b986549374544639a21ec2269579141.cwl b/.renku/workflow/4b986549374544639a21ec2269579141.cwl
new file mode 100644
index 000000000..08c8c8255
--- /dev/null
+++ b/.renku/workflow/4b986549374544639a21ec2269579141.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: states-metadata.json
+ streamable: false
+ type: string
+ input_3:
+ default: out_folder
+ streamable: false
+ type: string
+ input_4:
+ default: data/covidtracking
+ streamable: false
+ type: string
+ input_5:
+ default:
+ class: File
+ path: ../../notebooks/process/download-covidtracking-data.ipynb
+ streamable: false
+ type: File
+ input_6:
+ default: runs/download-covidtracking-data.runs.ipynb
+ streamable: false
+ type: string
+outputs:
+ output_1:
+ outputSource: step_3/output_0
+ streamable: false
+ type: File
+ output_2:
+ outputSource: step_3/output_1
+ streamable: false
+ type: Directory
+requirements: []
+steps:
+ step_1:
+ in:
+ filename: input_1
+ input_directory: step_3/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:
+ filename: input_2
+ input_directory: step_3/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: []
+ step_3:
+ in:
+ input_1: input_3
+ input_2: input_4
+ input_3: input_5
+ input_4: input_6
+ out:
+ - output_0
+ - output_1
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index 305d9455a..323c9bc1f 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 sha256:43110b45fbcaf372e87ef2da0578a7738d41ab1ef43c88163f61b52cd26d0c8f
-size 18921545
+oid sha256:c7ecdf2d64be4aa613b3159d8d7135e3794ed9d6cf5996465c2e9aa67de471ae
+size 18998763
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index cb98443aa..6637cf054 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 sha256:3856ce65b8cdf051d3887ddb14a1fed8c0ca94fa3028146ea446348f9ad7eec0
-size 112431
+oid sha256:f5ec84c44d9e948f34339a61f69a8f5fab844e8d0cb6824767001c8abeb475f9
+size 113826
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index b0388faba..2d849b575 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": 4.567062,
- "end_time": "2020-11-06T07:36:16.535139",
+ "duration": 4.17924,
+ "end_time": "2020-11-07T07:36:26.642620",
"exception": false,
- "start_time": "2020-11-06T07:36:11.968077",
+ "start_time": "2020-11-07T07:36:22.463380",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.021675,
- "end_time": "2020-11-06T07:36:16.571363",
+ "duration": 0.020794,
+ "end_time": "2020-11-07T07:36:26.676440",
"exception": false,
- "start_time": "2020-11-06T07:36:16.549688",
+ "start_time": "2020-11-07T07:36:26.655646",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.016527,
- "end_time": "2020-11-06T07:36:16.595797",
+ "duration": 0.018287,
+ "end_time": "2020-11-07T07:36:26.702242",
"exception": false,
- "start_time": "2020-11-06T07:36:16.579270",
+ "start_time": "2020-11-07T07:36:26.683955",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/cvg3ldzb/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/q9ded2bw/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": 0.004867,
- "end_time": "2020-11-06T07:36:16.605495",
+ "duration": 0.005456,
+ "end_time": "2020-11-07T07:36:26.713871",
"exception": false,
- "start_time": "2020-11-06T07:36:16.600628",
+ "start_time": "2020-11-07T07:36:26.708415",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.679735,
- "end_time": "2020-11-06T07:36:17.289998",
+ "duration": 0.677261,
+ "end_time": "2020-11-07T07:36:27.395390",
"exception": false,
- "start_time": "2020-11-06T07:36:16.610263",
+ "start_time": "2020-11-07T07:36:26.718129",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.022148,
- "end_time": "2020-11-06T07:36:17.323825",
+ "duration": 0.02652,
+ "end_time": "2020-11-07T07:36:27.435303",
"exception": false,
- "start_time": "2020-11-06T07:36:17.301677",
+ "start_time": "2020-11-07T07:36:27.408783",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.124039,
- "end_time": "2020-11-06T07:36:17.456351",
+ "duration": 0.071178,
+ "end_time": "2020-11-07T07:36:27.518446",
"exception": false,
- "start_time": "2020-11-06T07:36:17.332312",
+ "start_time": "2020-11-07T07:36:27.447268",
"status": "completed"
},
"tags": []
@@ -280,10 +280,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.006929,
- "end_time": "2020-11-06T07:36:17.474962",
+ "duration": 0.00671,
+ "end_time": "2020-11-07T07:36:27.536537",
"exception": false,
- "start_time": "2020-11-06T07:36:17.468033",
+ "start_time": "2020-11-07T07:36:27.529827",
"status": "completed"
},
"tags": []
@@ -297,10 +297,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.608193,
- "end_time": "2020-11-06T07:36:18.089165",
+ "duration": 0.457032,
+ "end_time": "2020-11-07T07:36:27.999709",
"exception": false,
- "start_time": "2020-11-06T07:36:17.480972",
+ "start_time": "2020-11-07T07:36:27.542677",
"status": "completed"
},
"tags": []
@@ -317,10 +317,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.041932,
- "end_time": "2020-11-06T07:36:18.146875",
+ "duration": 0.045366,
+ "end_time": "2020-11-07T07:36:28.059656",
"exception": false,
- "start_time": "2020-11-06T07:36:18.104943",
+ "start_time": "2020-11-07T07:36:28.014290",
"status": "completed"
},
"tags": []
@@ -339,10 +339,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.55035,
- "end_time": "2020-11-06T07:36:18.711417",
+ "duration": 0.545213,
+ "end_time": "2020-11-07T07:36:28.617366",
"exception": false,
- "start_time": "2020-11-06T07:36:18.161067",
+ "start_time": "2020-11-07T07:36:28.072153",
"status": "completed"
},
"tags": []
@@ -352,7 +352,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "13887 data points\n"
+ "13943 data points\n"
]
},
{
@@ -402,21 +402,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201105</td>\n",
+ " <td>20201106</td>\n",
" <td>AK</td>\n",
- " <td>18174.0</td>\n",
+ " <td>18699.0</td>\n",
" <td>NaN</td>\n",
- " <td>763652.0</td>\n",
+ " <td>762602.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>781826.0</td>\n",
- " <td>104.0</td>\n",
+ " <td>781301.0</td>\n",
+ " <td>106.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>781826</td>\n",
+ " <td>781301</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
- " <td>910e0e68ec1831715444823aa43d30e203d4ec90</td>\n",
+ " <td>c5e7641b5775740f5912af833d4d6b5c452c3383</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -426,21 +426,21 @@
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20201105</td>\n",
+ " <td>20201106</td>\n",
" <td>AL</td>\n",
- " <td>199158.0</td>\n",
- " <td>29892.0</td>\n",
- " <td>1209841.0</td>\n",
+ " <td>200714.0</td>\n",
+ " <td>30268.0</td>\n",
+ " <td>1217002.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1379107.0</td>\n",
- " <td>994.0</td>\n",
- " <td>21027.0</td>\n",
+ " <td>1387448.0</td>\n",
+ " <td>1022.0</td>\n",
+ " <td>21294.0</td>\n",
" <td>...</td>\n",
- " <td>1408999</td>\n",
- " <td>20</td>\n",
- " <td>0</td>\n",
- " <td>e660184b515c15867ae651a03b8c7f2f23271e52</td>\n",
+ " <td>1417716</td>\n",
+ " <td>23</td>\n",
+ " <td>267</td>\n",
+ " <td>3c28ba3b012f38332635f3629ab4fa30bddaf663</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -455,20 +455,20 @@
],
"text/plain": [
" date state positive probableCases negative pending \\\n",
- "0 20201105 AK 18174.0 NaN 763652.0 NaN \n",
- "1 20201105 AL 199158.0 29892.0 1209841.0 NaN \n",
+ "0 20201106 AK 18699.0 NaN 762602.0 NaN \n",
+ "1 20201106 AL 200714.0 30268.0 1217002.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 781826.0 104.0 \n",
- "1 totalTestsViral 1379107.0 994.0 \n",
+ "0 totalTestsViral 781301.0 106.0 \n",
+ "1 totalTestsViral 1387448.0 1022.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 NaN ... 781826 0 0 \n",
- "1 21027.0 ... 1408999 20 0 \n",
+ "0 NaN ... 781301 0 0 \n",
+ "1 21294.0 ... 1417716 23 267 \n",
"\n",
" hash commercialScore \\\n",
- "0 910e0e68ec1831715444823aa43d30e203d4ec90 0 \n",
- "1 e660184b515c15867ae651a03b8c7f2f23271e52 0 \n",
+ "0 c5e7641b5775740f5912af833d4d6b5c452c3383 0 \n",
+ "1 3c28ba3b012f38332635f3629ab4fa30bddaf663 0 \n",
"\n",
" negativeRegularScore negativeScore positiveScore score grade \n",
"0 0 0 0 0 \n",
@@ -508,18 +508,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 8.490223,
- "end_time": "2020-11-06T07:36:19.033810",
+ "duration": 8.158202,
+ "end_time": "2020-11-07T07:36:28.941551",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/cvg3ldzb/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/q9ded2bw/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/cvg3ldzb/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/q9ded2bw/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-11-06T07:36:10.543587",
+ "start_time": "2020-11-07T07:36:20.783349",
"version": "1.1.0"
}
},
--
GitLab