From fa683785e71abdca38980745cd189a22a7f63b77 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Wed, 17 Jun 2020 07:27:55 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../ff585315562b46b585b1de35c7438d42.cwl | 120 ++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 3 +
runs/download-covidtracking-data.runs.ipynb | 128 +++++++++---------
4 files changed, 189 insertions(+), 66 deletions(-)
create mode 100644 .renku/workflow/ff585315562b46b585b1de35c7438d42.cwl
create mode 100644 data/covidtracking/states-metadata.json
diff --git a/.renku/workflow/ff585315562b46b585b1de35c7438d42.cwl b/.renku/workflow/ff585315562b46b585b1de35c7438d42.cwl
new file mode 100644
index 000000000..7e97654a1
--- /dev/null
+++ b/.renku/workflow/ff585315562b46b585b1de35c7438d42.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_1
+ streamable: false
+ type: Directory
+ output_1:
+ outputSource: step_2/output_0
+ streamable: false
+ type: File
+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_1
+ - output_0
+ 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 99bc907c3..300bfe093 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:de60392a7baa2cc123ebdf0996a0ae8dfa9eae2cb696c53fa1c3337f00c074c2
-size 5053432
+oid sha256:0f32dd51a66472c808819f693cb2284fb3b10106be5b38534bd2fca2e27fc182
+size 5103450
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
new file mode 100644
index 000000000..59dc59a79
--- /dev/null
+++ b/data/covidtracking/states-metadata.json
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9ab397acedff8f0998303adf65381e02dda797f308a1cd826564dc7278c19127
+size 38218
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 0de9c2938..27e98ad11 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": 2.95574,
- "end_time": "2020-06-16T07:27:51.724896",
+ "duration": 1.866113,
+ "end_time": "2020-06-17T07:27:53.277271",
"exception": false,
- "start_time": "2020-06-16T07:27:48.769156",
+ "start_time": "2020-06-17T07:27:51.411158",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.025111,
- "end_time": "2020-06-16T07:27:51.765424",
+ "duration": 0.025595,
+ "end_time": "2020-06-17T07:27:53.317204",
"exception": false,
- "start_time": "2020-06-16T07:27:51.740313",
+ "start_time": "2020-06-17T07:27:53.291609",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.021459,
- "end_time": "2020-06-16T07:27:51.798841",
+ "duration": 0.026336,
+ "end_time": "2020-06-17T07:27:53.357601",
"exception": false,
- "start_time": "2020-06-16T07:27:51.777382",
+ "start_time": "2020-06-17T07:27:53.331265",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/65349t7c/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/um7bcmv4/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": 0.005489,
- "end_time": "2020-06-16T07:27:51.811094",
+ "duration": 0.007976,
+ "end_time": "2020-06-17T07:27:53.379933",
"exception": false,
- "start_time": "2020-06-16T07:27:51.805605",
+ "start_time": "2020-06-17T07:27:53.371957",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.178472,
- "end_time": "2020-06-16T07:27:51.995372",
+ "duration": 0.108755,
+ "end_time": "2020-06-17T07:27:53.495212",
"exception": false,
- "start_time": "2020-06-16T07:27:51.816900",
+ "start_time": "2020-06-17T07:27:53.386457",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.024849,
- "end_time": "2020-06-16T07:27:52.034982",
+ "duration": 0.026513,
+ "end_time": "2020-06-17T07:27:53.537059",
"exception": false,
- "start_time": "2020-06-16T07:27:52.010133",
+ "start_time": "2020-06-17T07:27:53.510546",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.073662,
- "end_time": "2020-06-16T07:27:52.119682",
+ "duration": 0.074462,
+ "end_time": "2020-06-17T07:27:53.623699",
"exception": false,
- "start_time": "2020-06-16T07:27:52.046020",
+ "start_time": "2020-06-17T07:27:53.549237",
"status": "completed"
},
"tags": []
@@ -249,10 +249,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008628,
- "end_time": "2020-06-16T07:27:52.142661",
+ "duration": 0.008079,
+ "end_time": "2020-06-17T07:27:53.646468",
"exception": false,
- "start_time": "2020-06-16T07:27:52.134033",
+ "start_time": "2020-06-17T07:27:53.638389",
"status": "completed"
},
"tags": []
@@ -266,10 +266,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.290266,
- "end_time": "2020-06-16T07:27:52.439950",
+ "duration": 0.194752,
+ "end_time": "2020-06-17T07:27:53.847777",
"exception": false,
- "start_time": "2020-06-16T07:27:52.149684",
+ "start_time": "2020-06-17T07:27:53.653025",
"status": "completed"
},
"tags": []
@@ -286,10 +286,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.030335,
- "end_time": "2020-06-16T07:27:52.488533",
+ "duration": 0.036515,
+ "end_time": "2020-06-17T07:27:53.905748",
"exception": false,
- "start_time": "2020-06-16T07:27:52.458198",
+ "start_time": "2020-06-17T07:27:53.869233",
"status": "completed"
},
"tags": []
@@ -308,10 +308,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.196926,
- "end_time": "2020-06-16T07:27:52.697767",
+ "duration": 0.239508,
+ "end_time": "2020-06-17T07:27:54.163296",
"exception": false,
- "start_time": "2020-06-16T07:27:52.500841",
+ "start_time": "2020-06-17T07:27:53.923788",
"status": "completed"
},
"tags": []
@@ -321,7 +321,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "5729 data points\n"
+ "5785 data points\n"
]
},
{
@@ -371,21 +371,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200615</td>\n",
+ " <td>20200616</td>\n",
" <td>AK</td>\n",
- " <td>664.0</td>\n",
- " <td>73773.0</td>\n",
+ " <td>676.0</td>\n",
+ " <td>75539.0</td>\n",
" <td>NaN</td>\n",
- " <td>21.0</td>\n",
+ " <td>22.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>3.0</td>\n",
+ " <td>2.0</td>\n",
" <td>...</td>\n",
- " <td>74437</td>\n",
+ " <td>76215</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
- " <td>6b08035ecccc3d7c158bd1ebff8a325714b92a03</td>\n",
+ " <td>9ce63702a549318053a366a0ef2d97680c2e6bad</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -395,21 +395,21 @@
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200615</td>\n",
+ " <td>20200616</td>\n",
" <td>AL</td>\n",
- " <td>26272.0</td>\n",
- " <td>276402.0</td>\n",
+ " <td>26912.0</td>\n",
+ " <td>278512.0</td>\n",
" <td>NaN</td>\n",
- " <td>546.0</td>\n",
- " <td>2259.0</td>\n",
+ " <td>678.0</td>\n",
+ " <td>2315.0</td>\n",
" <td>NaN</td>\n",
- " <td>676.0</td>\n",
+ " <td>682.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>302674</td>\n",
- " <td>1</td>\n",
- " <td>4</td>\n",
- " <td>5a2e19c16964661d50217b2850723b167c2255b8</td>\n",
+ " <td>305424</td>\n",
+ " <td>11</td>\n",
+ " <td>56</td>\n",
+ " <td>e76cb0a1b1984ba8a95f80bd42da175e42add663</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -424,20 +424,20 @@
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200615 AK 664.0 73773.0 NaN 21.0 \n",
- "1 20200615 AL 26272.0 276402.0 NaN 546.0 \n",
+ "0 20200616 AK 676.0 75539.0 NaN 22.0 \n",
+ "1 20200616 AL 26912.0 278512.0 NaN 678.0 \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 2259.0 NaN 676.0 \n",
+ "1 2315.0 NaN 682.0 \n",
"\n",
" onVentilatorCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 3.0 ... 74437 0 0 \n",
- "1 NaN ... 302674 1 4 \n",
+ "0 2.0 ... 76215 0 0 \n",
+ "1 NaN ... 305424 11 56 \n",
"\n",
" hash commercialScore \\\n",
- "0 6b08035ecccc3d7c158bd1ebff8a325714b92a03 0 \n",
- "1 5a2e19c16964661d50217b2850723b167c2255b8 0 \n",
+ "0 9ce63702a549318053a366a0ef2d97680c2e6bad 0 \n",
+ "1 e76cb0a1b1984ba8a95f80bd42da175e42add663 0 \n",
"\n",
" negativeRegularScore negativeScore positiveScore score grade \n",
"0 0 0 0 0 \n",
@@ -477,18 +477,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 5.92134,
- "end_time": "2020-06-16T07:27:53.024491",
+ "duration": 5.103315,
+ "end_time": "2020-06-17T07:27:54.492913",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/65349t7c/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/um7bcmv4/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/65349t7c/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/um7bcmv4/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-06-16T07:27:47.103151",
+ "start_time": "2020-06-17T07:27:49.389598",
"version": "1.1.0"
}
},
--
GitLab