From 861edaf7e86388e387dbbcd09bb8aeac428d7672 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Thu, 22 Oct 2020 07:38:28 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../9f59547fd69f4f239592080ba6152060.cwl | 120 ++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 134 +++++++++---------
4 files changed, 191 insertions(+), 71 deletions(-)
create mode 100644 .renku/workflow/9f59547fd69f4f239592080ba6152060.cwl
diff --git a/.renku/workflow/9f59547fd69f4f239592080ba6152060.cwl b/.renku/workflow/9f59547fd69f4f239592080ba6152060.cwl
new file mode 100644
index 000000000..95851678e
--- /dev/null
+++ b/.renku/workflow/9f59547fd69f4f239592080ba6152060.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: 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-metadata.json
+ streamable: false
+ type: string
+outputs:
+ output_0:
+ 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-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:
+ 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-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 0008f183c..f46f8a866 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 sha256:7624a1e2c0951c2035a1829476c0773330956c8d75eaba8721497f733d16e617
-size 17510251
+oid sha256:df494539d1f415fa97fa4b797e19b344b77a38a26859da7c18709fa6ef5c3610
+size 17664123
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 8a80f9556..3c031130f 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:a2a702050c15a7b89f480f9a5985d58a3620ad50b21497614fdaecbfcc82b10d
-size 99417
+oid sha256:47af66a052f4bec5112aa6c8fb497518f1e5824d70ba73e3707e0771e792462b
+size 101226
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index cc45a47e9..ac34098ef 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": 5.449118,
- "end_time": "2020-10-20T07:38:33.046345",
+ "duration": 3.694958,
+ "end_time": "2020-10-22T07:37:56.023202",
"exception": false,
- "start_time": "2020-10-20T07:38:27.597227",
+ "start_time": "2020-10-22T07:37:52.328244",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.02487,
- "end_time": "2020-10-20T07:38:33.088422",
+ "duration": 0.021365,
+ "end_time": "2020-10-22T07:37:56.058979",
"exception": false,
- "start_time": "2020-10-20T07:38:33.063552",
+ "start_time": "2020-10-22T07:37:56.037614",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.020621,
- "end_time": "2020-10-20T07:38:33.120588",
+ "duration": 0.020356,
+ "end_time": "2020-10-22T07:37:56.091110",
"exception": false,
- "start_time": "2020-10-20T07:38:33.099967",
+ "start_time": "2020-10-22T07:37:56.070754",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/m_poq3ob/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/apxgwusv/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": 0.006555,
- "end_time": "2020-10-20T07:38:33.134837",
+ "duration": 0.008373,
+ "end_time": "2020-10-22T07:37:56.107673",
"exception": false,
- "start_time": "2020-10-20T07:38:33.128282",
+ "start_time": "2020-10-22T07:37:56.099300",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.794016,
- "end_time": "2020-10-20T07:38:33.936386",
+ "duration": 0.597843,
+ "end_time": "2020-10-22T07:37:56.713092",
"exception": false,
- "start_time": "2020-10-20T07:38:33.142370",
+ "start_time": "2020-10-22T07:37:56.115249",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.02949,
- "end_time": "2020-10-20T07:38:33.980536",
+ "duration": 0.024803,
+ "end_time": "2020-10-22T07:37:56.749344",
"exception": false,
- "start_time": "2020-10-20T07:38:33.951046",
+ "start_time": "2020-10-22T07:37:56.724541",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.108349,
- "end_time": "2020-10-20T07:38:34.102052",
+ "duration": 0.078335,
+ "end_time": "2020-10-22T07:37:56.837651",
"exception": false,
- "start_time": "2020-10-20T07:38:33.993703",
+ "start_time": "2020-10-22T07:37:56.759316",
"status": "completed"
},
"tags": []
@@ -280,10 +280,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007961,
- "end_time": "2020-10-20T07:38:34.124356",
+ "duration": 0.008528,
+ "end_time": "2020-10-22T07:37:56.855640",
"exception": false,
- "start_time": "2020-10-20T07:38:34.116395",
+ "start_time": "2020-10-22T07:37:56.847112",
"status": "completed"
},
"tags": []
@@ -297,10 +297,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.784791,
- "end_time": "2020-10-20T07:38:34.915703",
+ "duration": 29.269064,
+ "end_time": "2020-10-22T07:38:26.133112",
"exception": false,
- "start_time": "2020-10-20T07:38:34.130912",
+ "start_time": "2020-10-22T07:37:56.864048",
"status": "completed"
},
"tags": []
@@ -317,10 +317,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.069935,
- "end_time": "2020-10-20T07:38:35.003603",
+ "duration": 0.05645,
+ "end_time": "2020-10-22T07:38:26.205885",
"exception": false,
- "start_time": "2020-10-20T07:38:34.933668",
+ "start_time": "2020-10-22T07:38:26.149435",
"status": "completed"
},
"tags": []
@@ -339,10 +339,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.627771,
- "end_time": "2020-10-20T07:38:35.647579",
+ "duration": 0.688088,
+ "end_time": "2020-10-22T07:38:26.905147",
"exception": false,
- "start_time": "2020-10-20T07:38:35.019808",
+ "start_time": "2020-10-22T07:38:26.217059",
"status": "completed"
},
"tags": []
@@ -352,7 +352,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "12877 data points\n"
+ "12989 data points\n"
]
},
{
@@ -402,21 +402,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201019</td>\n",
+ " <td>20201021</td>\n",
" <td>AK</td>\n",
- " <td>12220.0</td>\n",
+ " <td>12644.0</td>\n",
" <td>NaN</td>\n",
- " <td>524003.0</td>\n",
+ " <td>534496.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>536223.0</td>\n",
- " <td>65.0</td>\n",
+ " <td>547140.0</td>\n",
+ " <td>41.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>536223</td>\n",
- " <td>0</td>\n",
+ " <td>547140</td>\n",
+ " <td>1</td>\n",
" <td>0</td>\n",
- " <td>69b847e0fe9b05ba3cc485d576949b9ea2f59cfb</td>\n",
+ " <td>4d2eabde0cdfbe86ede9f58509002a80af61be19</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>20201019</td>\n",
+ " <td>20201021</td>\n",
" <td>AL</td>\n",
- " <td>173485.0</td>\n",
- " <td>21213.0</td>\n",
- " <td>1107828.0</td>\n",
+ " <td>174528.0</td>\n",
+ " <td>21512.0</td>\n",
+ " <td>1120507.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1260100.0</td>\n",
- " <td>859.0</td>\n",
- " <td>19081.0</td>\n",
+ " <td>1273523.0</td>\n",
+ " <td>863.0</td>\n",
+ " <td>19330.0</td>\n",
" <td>...</td>\n",
- " <td>1281313</td>\n",
- " <td>1</td>\n",
- " <td>226</td>\n",
- " <td>622efeb21f69f1714609d5c58da3fe7fb9562b13</td>\n",
+ " <td>1295035</td>\n",
+ " <td>0</td>\n",
+ " <td>249</td>\n",
+ " <td>132b6a5489c29acc31311d7a21bf462b2584f59e</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 20201019 AK 12220.0 NaN 524003.0 NaN \n",
- "1 20201019 AL 173485.0 21213.0 1107828.0 NaN \n",
+ "0 20201021 AK 12644.0 NaN 534496.0 NaN \n",
+ "1 20201021 AL 174528.0 21512.0 1120507.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 536223.0 65.0 \n",
- "1 totalTestsViral 1260100.0 859.0 \n",
+ "0 totalTestsViral 547140.0 41.0 \n",
+ "1 totalTestsViral 1273523.0 863.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 NaN ... 536223 0 0 \n",
- "1 19081.0 ... 1281313 1 226 \n",
+ "0 NaN ... 547140 1 0 \n",
+ "1 19330.0 ... 1295035 0 249 \n",
"\n",
" hash commercialScore \\\n",
- "0 69b847e0fe9b05ba3cc485d576949b9ea2f59cfb 0 \n",
- "1 622efeb21f69f1714609d5c58da3fe7fb9562b13 0 \n",
+ "0 4d2eabde0cdfbe86ede9f58509002a80af61be19 0 \n",
+ "1 132b6a5489c29acc31311d7a21bf462b2584f59e 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": 11.263281,
- "end_time": "2020-10-20T07:38:36.075825",
+ "duration": 36.497579,
+ "end_time": "2020-10-22T07:38:27.226206",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/m_poq3ob/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/apxgwusv/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/m_poq3ob/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/apxgwusv/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-10-20T07:38:24.812544",
+ "start_time": "2020-10-22T07:37:50.728627",
"version": "1.1.0"
}
},
--
GitLab