From def418966f59fb64d92344f523b21fca408e96b1 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Fri, 20 Nov 2020 07:42:22 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../f7f923e1a3704e6285fde7b2c1b1cdc2.cwl | 120 +++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 138 +++++++++---------
4 files changed, 193 insertions(+), 73 deletions(-)
create mode 100644 .renku/workflow/f7f923e1a3704e6285fde7b2c1b1cdc2.cwl
diff --git a/.renku/workflow/f7f923e1a3704e6285fde7b2c1b1cdc2.cwl b/.renku/workflow/f7f923e1a3704e6285fde7b2c1b1cdc2.cwl
new file mode 100644
index 000000000..fca0574fb
--- /dev/null
+++ b/.renku/workflow/f7f923e1a3704e6285fde7b2c1b1cdc2.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_2:
+ 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 5a4c39b8d..87b89f934 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 sha256:8b866cf469f888381452245a3b1c3c68cd034b8634323f09cf555ed8d9326565
-size 19927027
+oid sha256:5554dd423ed693475fcbcfba496440aea84018f5f0bd6e4f14acba79b7373f83
+size 20004386
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index b10317d8c..24826d5a3 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 sha256:33e155b3aa51ca99e45360ddb826f65d77e4068eac535de1e85f1d7e3542de2b
-size 127157
+oid sha256:23afc771d7e7037493344a6b194cc893a1ebc2bb47f498a6f0026134963c3342
+size 126837
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index d897315a2..f85c24e9c 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": 4.896635,
- "end_time": "2020-11-19T07:37:54.448471",
+ "duration": 6.685221,
+ "end_time": "2020-11-20T07:42:18.592945",
"exception": false,
- "start_time": "2020-11-19T07:37:49.551836",
+ "start_time": "2020-11-20T07:42:11.907724",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.023118,
- "end_time": "2020-11-19T07:37:54.486846",
+ "duration": 0.021916,
+ "end_time": "2020-11-20T07:42:18.631634",
"exception": false,
- "start_time": "2020-11-19T07:37:54.463728",
+ "start_time": "2020-11-20T07:42:18.609718",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.021391,
- "end_time": "2020-11-19T07:37:54.520861",
+ "duration": 0.018925,
+ "end_time": "2020-11-20T07:42:18.666305",
"exception": false,
- "start_time": "2020-11-19T07:37:54.499470",
+ "start_time": "2020-11-20T07:42:18.647380",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/oujakx8z/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/4nizuviw/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": 0.006516,
- "end_time": "2020-11-19T07:37:54.536383",
+ "duration": 0.006326,
+ "end_time": "2020-11-20T07:42:18.679382",
"exception": false,
- "start_time": "2020-11-19T07:37:54.529867",
+ "start_time": "2020-11-20T07:42:18.673056",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.782228,
- "end_time": "2020-11-19T07:37:55.324696",
+ "duration": 0.817947,
+ "end_time": "2020-11-20T07:42:19.513184",
"exception": false,
- "start_time": "2020-11-19T07:37:54.542468",
+ "start_time": "2020-11-20T07:42:18.695237",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.02224,
- "end_time": "2020-11-19T07:37:55.358732",
+ "duration": 0.021783,
+ "end_time": "2020-11-20T07:42:19.545211",
"exception": false,
- "start_time": "2020-11-19T07:37:55.336492",
+ "start_time": "2020-11-20T07:42:19.523428",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.096108,
- "end_time": "2020-11-19T07:37:55.464558",
+ "duration": 0.091027,
+ "end_time": "2020-11-20T07:42:19.645836",
"exception": false,
- "start_time": "2020-11-19T07:37:55.368450",
+ "start_time": "2020-11-20T07:42:19.554809",
"status": "completed"
},
"tags": []
@@ -284,10 +284,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007767,
- "end_time": "2020-11-19T07:37:55.485516",
+ "duration": 0.010459,
+ "end_time": "2020-11-20T07:42:19.668290",
"exception": false,
- "start_time": "2020-11-19T07:37:55.477749",
+ "start_time": "2020-11-20T07:42:19.657831",
"status": "completed"
},
"tags": []
@@ -301,10 +301,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.603939,
- "end_time": "2020-11-19T07:37:56.095902",
+ "duration": 0.670368,
+ "end_time": "2020-11-20T07:42:20.345522",
"exception": false,
- "start_time": "2020-11-19T07:37:55.491963",
+ "start_time": "2020-11-20T07:42:19.675154",
"status": "completed"
},
"tags": []
@@ -321,10 +321,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.06203,
- "end_time": "2020-11-19T07:37:56.173711",
+ "duration": 0.072759,
+ "end_time": "2020-11-20T07:42:20.429591",
"exception": false,
- "start_time": "2020-11-19T07:37:56.111681",
+ "start_time": "2020-11-20T07:42:20.356832",
"status": "completed"
},
"tags": []
@@ -343,10 +343,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.571345,
- "end_time": "2020-11-19T07:37:56.759551",
+ "duration": 0.844439,
+ "end_time": "2020-11-20T07:42:21.285058",
"exception": false,
- "start_time": "2020-11-19T07:37:56.188206",
+ "start_time": "2020-11-20T07:42:20.440619",
"status": "completed"
},
"tags": []
@@ -356,7 +356,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "14617 data points\n"
+ "14673 data points\n"
]
},
{
@@ -406,21 +406,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201118</td>\n",
+ " <td>20201119</td>\n",
" <td>AK</td>\n",
- " <td>24419.0</td>\n",
+ " <td>24909.0</td>\n",
" <td>NaN</td>\n",
- " <td>861139.0</td>\n",
+ " <td>873890.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>885558.0</td>\n",
- " <td>147.0</td>\n",
- " <td>584.0</td>\n",
+ " <td>898799.0</td>\n",
+ " <td>139.0</td>\n",
+ " <td>593.0</td>\n",
" <td>...</td>\n",
- " <td>885558</td>\n",
- " <td>0</td>\n",
- " <td>22</td>\n",
- " <td>959c531cf9b1dd6d6e9852ef8674d6e5cc0cde51</td>\n",
+ " <td>898799</td>\n",
+ " <td>1</td>\n",
+ " <td>9</td>\n",
+ " <td>dd60caa3c0b65aa928204156ef405a95116f3f03</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -430,21 +430,21 @@
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20201118</td>\n",
+ " <td>20201119</td>\n",
" <td>AL</td>\n",
- " <td>223486.0</td>\n",
- " <td>35863.0</td>\n",
- " <td>1294045.0</td>\n",
+ " <td>225910.0</td>\n",
+ " <td>36449.0</td>\n",
+ " <td>1307256.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1481668.0</td>\n",
- " <td>1303.0</td>\n",
- " <td>23088.0</td>\n",
+ " <td>1496717.0</td>\n",
+ " <td>1315.0</td>\n",
+ " <td>23295.0</td>\n",
" <td>...</td>\n",
- " <td>1517531</td>\n",
- " <td>46</td>\n",
- " <td>372</td>\n",
- " <td>670bf40671e729deeede1278bfeeb631084588b3</td>\n",
+ " <td>1533166</td>\n",
+ " <td>72</td>\n",
+ " <td>207</td>\n",
+ " <td>087ae3543d37e84035c1fde2ac39d1cec933e88d</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -459,20 +459,20 @@
],
"text/plain": [
" date state positive probableCases negative pending \\\n",
- "0 20201118 AK 24419.0 NaN 861139.0 NaN \n",
- "1 20201118 AL 223486.0 35863.0 1294045.0 NaN \n",
+ "0 20201119 AK 24909.0 NaN 873890.0 NaN \n",
+ "1 20201119 AL 225910.0 36449.0 1307256.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 885558.0 147.0 \n",
- "1 totalTestsViral 1481668.0 1303.0 \n",
+ "0 totalTestsViral 898799.0 139.0 \n",
+ "1 totalTestsViral 1496717.0 1315.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 584.0 ... 885558 0 22 \n",
- "1 23088.0 ... 1517531 46 372 \n",
+ "0 593.0 ... 898799 1 9 \n",
+ "1 23295.0 ... 1533166 72 207 \n",
"\n",
" hash commercialScore \\\n",
- "0 959c531cf9b1dd6d6e9852ef8674d6e5cc0cde51 0 \n",
- "1 670bf40671e729deeede1278bfeeb631084588b3 0 \n",
+ "0 dd60caa3c0b65aa928204156ef405a95116f3f03 0 \n",
+ "1 087ae3543d37e84035c1fde2ac39d1cec933e88d 0 \n",
"\n",
" negativeRegularScore negativeScore positiveScore score grade \n",
"0 0 0 0 0 \n",
@@ -512,18 +512,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 9.392625,
- "end_time": "2020-11-19T07:37:57.084090",
+ "duration": 12.646574,
+ "end_time": "2020-11-20T07:42:21.715206",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/oujakx8z/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/4nizuviw/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/oujakx8z/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/4nizuviw/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-11-19T07:37:47.691465",
+ "start_time": "2020-11-20T07:42:09.068632",
"version": "1.1.0"
}
},
--
GitLab