From 3ca155e7837b5f9d81d8c9a56b7851779f43079e Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Sun, 13 Dec 2020 07:37:48 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../4362ea2d18ab490fa0e5d65099217267.cwl | 120 ++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 130 +++++++++---------
4 files changed, 189 insertions(+), 69 deletions(-)
create mode 100644 .renku/workflow/4362ea2d18ab490fa0e5d65099217267.cwl
diff --git a/.renku/workflow/4362ea2d18ab490fa0e5d65099217267.cwl b/.renku/workflow/4362ea2d18ab490fa0e5d65099217267.cwl
new file mode 100644
index 000000000..5cbdadca0
--- /dev/null
+++ b/.renku/workflow/4362ea2d18ab490fa0e5d65099217267.cwl
@@ -0,0 +1,120 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: out_folder
+ 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: states-metadata.json
+ streamable: false
+ type: string
+ input_6:
+ default: states-daily.json
+ streamable: false
+ type: string
+outputs:
+ output_2:
+ outputSource: step_1/output_1
+ streamable: false
+ type: Directory
+ output_3:
+ outputSource: step_1/output_0
+ streamable: false
+ type: File
+requirements: []
+steps:
+ step_1:
+ in:
+ input_1: input_1
+ input_2: input_2
+ input_3: input_3
+ input_4: input_4
+ out:
+ - output_1
+ - output_0
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
+ step_2:
+ in:
+ filename: input_5
+ 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
+ class: InlineJavascriptRequirement
+ - &id002
+ class: InitialWorkDirRequirement
+ listing: $(inputs.input_directory.listing)
+ successCodes: []
+ temporaryFailCodes: []
+ step_3:
+ in:
+ filename: input_6
+ input_directory: step_1/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 b155be792..3e31bc293 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:e62d080a170bc871e31539c8be8b3cdd3658cbe5d7fcf8a589eee3aefd0209e4
-size 21724952
+oid sha256:6834cb04ee15ed650960ef5b8d6f14b8fb6b801f46fd0d8b7970b1d163750d72
+size 21802399
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 4a863b13d..2d34465ee 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:f2f507c8365cc03aedb8456a10e41bdea80f74fbd6ed14b16746c6968065691b
-size 150268
+oid sha256:7354c67941de362dc05fa040ab2f436300cb1d766c501671e16643a447f1ec46
+size 151830
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index ba4c0680b..7a1003c03 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": 6.889652,
- "end_time": "2020-12-12T07:38:05.389643",
+ "duration": 5.223516,
+ "end_time": "2020-12-13T07:37:44.521551",
"exception": false,
- "start_time": "2020-12-12T07:37:58.499991",
+ "start_time": "2020-12-13T07:37:39.298035",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.015644,
- "end_time": "2020-12-12T07:38:05.417406",
+ "duration": 0.020038,
+ "end_time": "2020-12-13T07:37:44.555668",
"exception": false,
- "start_time": "2020-12-12T07:38:05.401762",
+ "start_time": "2020-12-13T07:37:44.535630",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.010775,
- "end_time": "2020-12-12T07:38:05.433035",
+ "duration": 0.016584,
+ "end_time": "2020-12-13T07:37:44.579810",
"exception": false,
- "start_time": "2020-12-12T07:38:05.422260",
+ "start_time": "2020-12-13T07:37:44.563226",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/r6lieysd/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/_2i_io6h/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": 0.004017,
- "end_time": "2020-12-12T07:38:05.441138",
+ "duration": 0.005697,
+ "end_time": "2020-12-13T07:37:44.591532",
"exception": false,
- "start_time": "2020-12-12T07:38:05.437121",
+ "start_time": "2020-12-13T07:37:44.585835",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.343477,
- "end_time": "2020-12-12T07:38:05.788838",
+ "duration": 1.048541,
+ "end_time": "2020-12-13T07:37:45.645366",
"exception": false,
- "start_time": "2020-12-12T07:38:05.445361",
+ "start_time": "2020-12-13T07:37:44.596825",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.022185,
- "end_time": "2020-12-12T07:38:05.822402",
+ "duration": 0.024147,
+ "end_time": "2020-12-13T07:37:45.682788",
"exception": false,
- "start_time": "2020-12-12T07:38:05.800217",
+ "start_time": "2020-12-13T07:37:45.658641",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.071164,
- "end_time": "2020-12-12T07:38:05.902998",
+ "duration": 0.083844,
+ "end_time": "2020-12-13T07:37:45.779457",
"exception": false,
- "start_time": "2020-12-12T07:38:05.831834",
+ "start_time": "2020-12-13T07:37:45.695613",
"status": "completed"
},
"tags": []
@@ -284,10 +284,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.006768,
- "end_time": "2020-12-12T07:38:05.921404",
+ "duration": 0.008011,
+ "end_time": "2020-12-13T07:37:45.801291",
"exception": false,
- "start_time": "2020-12-12T07:38:05.914636",
+ "start_time": "2020-12-13T07:37:45.793280",
"status": "completed"
},
"tags": []
@@ -301,10 +301,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.644425,
- "end_time": "2020-12-12T07:38:06.571920",
+ "duration": 0.679409,
+ "end_time": "2020-12-13T07:37:46.487312",
"exception": false,
- "start_time": "2020-12-12T07:38:05.927495",
+ "start_time": "2020-12-13T07:37:45.807903",
"status": "completed"
},
"tags": []
@@ -321,10 +321,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.050735,
- "end_time": "2020-12-12T07:38:06.639504",
+ "duration": 0.046951,
+ "end_time": "2020-12-13T07:37:46.549317",
"exception": false,
- "start_time": "2020-12-12T07:38:06.588769",
+ "start_time": "2020-12-13T07:37:46.502366",
"status": "completed"
},
"tags": []
@@ -343,10 +343,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.614728,
- "end_time": "2020-12-12T07:38:07.266668",
+ "duration": 0.607161,
+ "end_time": "2020-12-13T07:37:47.168953",
"exception": false,
- "start_time": "2020-12-12T07:38:06.651940",
+ "start_time": "2020-12-13T07:37:46.561792",
"status": "completed"
},
"tags": []
@@ -356,7 +356,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "15913 data points\n"
+ "15969 data points\n"
]
},
{
@@ -406,21 +406,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201211</td>\n",
+ " <td>20201212</td>\n",
" <td>AK</td>\n",
- " <td>38584.0</td>\n",
+ " <td>39101.0</td>\n",
" <td>NaN</td>\n",
- " <td>1084961.0</td>\n",
+ " <td>1094317.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1123545.0</td>\n",
+ " <td>1133418.0</td>\n",
" <td>146.0</td>\n",
- " <td>869.0</td>\n",
+ " <td>883.0</td>\n",
" <td>...</td>\n",
- " <td>1123545</td>\n",
- " <td>3</td>\n",
- " <td>9</td>\n",
- " <td>47f2cb8f9f01019549b85b0450c8c42c15bb3e77</td>\n",
+ " <td>1133418</td>\n",
+ " <td>18</td>\n",
+ " <td>14</td>\n",
+ " <td>a2d18ec064bf83b8ac5c9f93a2e0e38827d0865b</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>20201211</td>\n",
+ " <td>20201212</td>\n",
" <td>AL</td>\n",
- " <td>288775.0</td>\n",
- " <td>50896.0</td>\n",
+ " <td>292841.0</td>\n",
+ " <td>52306.0</td>\n",
" <td>1458560.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsPeopleViral</td>\n",
" <td>1696439.0</td>\n",
- " <td>2111.0</td>\n",
+ " <td>2161.0</td>\n",
" <td>28146.0</td>\n",
" <td>...</td>\n",
- " <td>1747335</td>\n",
- " <td>52</td>\n",
- " <td>528</td>\n",
- " <td>3bf1ccc167c9d139e7506942ea8f53c42bdeeab7</td>\n",
+ " <td>1751401</td>\n",
+ " <td>16</td>\n",
+ " <td>0</td>\n",
+ " <td>660f90fe723b05c91856029bfd46d43423c107e2</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 20201211 AK 38584.0 NaN 1084961.0 NaN \n",
- "1 20201211 AL 288775.0 50896.0 1458560.0 NaN \n",
+ "0 20201212 AK 39101.0 NaN 1094317.0 NaN \n",
+ "1 20201212 AL 292841.0 52306.0 1458560.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 1123545.0 146.0 \n",
- "1 totalTestsPeopleViral 1696439.0 2111.0 \n",
+ "0 totalTestsViral 1133418.0 146.0 \n",
+ "1 totalTestsPeopleViral 1696439.0 2161.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 869.0 ... 1123545 3 9 \n",
- "1 28146.0 ... 1747335 52 528 \n",
+ "0 883.0 ... 1133418 18 14 \n",
+ "1 28146.0 ... 1751401 16 0 \n",
"\n",
" hash commercialScore \\\n",
- "0 47f2cb8f9f01019549b85b0450c8c42c15bb3e77 0 \n",
- "1 3bf1ccc167c9d139e7506942ea8f53c42bdeeab7 0 \n",
+ "0 a2d18ec064bf83b8ac5c9f93a2e0e38827d0865b 0 \n",
+ "1 660f90fe723b05c91856029bfd46d43423c107e2 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": 10.7272,
- "end_time": "2020-12-12T07:38:07.588984",
+ "duration": 9.926778,
+ "end_time": "2020-12-13T07:37:47.490053",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/r6lieysd/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/_2i_io6h/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/r6lieysd/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/_2i_io6h/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-12-12T07:37:56.861784",
+ "start_time": "2020-12-13T07:37:37.563275",
"version": "1.1.0"
}
},
--
GitLab