From aab343e86dba51a6339c2ff72d4c42149e4965c0 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Thu, 6 Aug 2020 07:32:31 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../e9dce04f985d403582259868f7c5f7cb.cwl | 120 +++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 124 +++++++++---------
4 files changed, 186 insertions(+), 66 deletions(-)
create mode 100644 .renku/workflow/e9dce04f985d403582259868f7c5f7cb.cwl
diff --git a/.renku/workflow/e9dce04f985d403582259868f7c5f7cb.cwl b/.renku/workflow/e9dce04f985d403582259868f7c5f7cb.cwl
new file mode 100644
index 000000000..855541b73
--- /dev/null
+++ b/.renku/workflow/e9dce04f985d403582259868f7c5f7cb.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_1:
+ 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 b651e7865..4e3362939 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 sha256:3c176e31513d08dbf8d4e7af65cd1eb8a248b1c36c344bae39e7e2dd9a3e7410
-size 7922705
+oid sha256:157ea87a5e7a61335b9fc48a50577ac43ef0bce919622996f0e51176e5d1e01a
+size 7975364
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 4dfd520f5..c96a14c3f 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 sha256:260a3d2511a33a3c73ad023e9856bcc6ea3276e38025017272db886c52e0a5be
-size 57814
+oid sha256:ebba936994c56fd0e6e971917ebe1e08e5d48143d430ce6e2aa4ec2d2e0972f0
+size 58914
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 572fb57d6..33071a060 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": 3.880489,
- "end_time": "2020-08-05T07:33:37.928356",
+ "duration": 4.25667,
+ "end_time": "2020-08-06T07:32:29.957512",
"exception": false,
- "start_time": "2020-08-05T07:33:34.047867",
+ "start_time": "2020-08-06T07:32:25.700842",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.024466,
- "end_time": "2020-08-05T07:33:37.961210",
+ "duration": 0.020099,
+ "end_time": "2020-08-06T07:32:29.990655",
"exception": false,
- "start_time": "2020-08-05T07:33:37.936744",
+ "start_time": "2020-08-06T07:32:29.970556",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.024783,
- "end_time": "2020-08-05T07:33:37.993930",
+ "duration": 0.019877,
+ "end_time": "2020-08-06T07:32:30.019779",
"exception": false,
- "start_time": "2020-08-05T07:33:37.969147",
+ "start_time": "2020-08-06T07:32:29.999902",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/ooj1q6z_/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/y8yxp7e2/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": 0.007393,
- "end_time": "2020-08-05T07:33:38.011199",
+ "duration": 0.007191,
+ "end_time": "2020-08-06T07:32:30.035387",
"exception": false,
- "start_time": "2020-08-05T07:33:38.003806",
+ "start_time": "2020-08-06T07:32:30.028196",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.174305,
- "end_time": "2020-08-05T07:33:38.191736",
+ "duration": 0.067951,
+ "end_time": "2020-08-06T07:32:30.110740",
"exception": false,
- "start_time": "2020-08-05T07:33:38.017431",
+ "start_time": "2020-08-06T07:32:30.042789",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.030909,
- "end_time": "2020-08-05T07:33:38.238139",
+ "duration": 0.022383,
+ "end_time": "2020-08-06T07:32:30.144709",
"exception": false,
- "start_time": "2020-08-05T07:33:38.207230",
+ "start_time": "2020-08-06T07:32:30.122326",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.081414,
- "end_time": "2020-08-05T07:33:38.332447",
+ "duration": 0.09242,
+ "end_time": "2020-08-06T07:32:30.245483",
"exception": false,
- "start_time": "2020-08-05T07:33:38.251033",
+ "start_time": "2020-08-06T07:32:30.153063",
"status": "completed"
},
"tags": []
@@ -249,10 +249,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008205,
- "end_time": "2020-08-05T07:33:38.352814",
+ "duration": 0.008447,
+ "end_time": "2020-08-06T07:32:30.264032",
"exception": false,
- "start_time": "2020-08-05T07:33:38.344609",
+ "start_time": "2020-08-06T07:32:30.255585",
"status": "completed"
},
"tags": []
@@ -266,10 +266,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.242617,
- "end_time": "2020-08-05T07:33:38.602651",
+ "duration": 0.272467,
+ "end_time": "2020-08-06T07:32:30.545373",
"exception": false,
- "start_time": "2020-08-05T07:33:38.360034",
+ "start_time": "2020-08-06T07:32:30.272906",
"status": "completed"
},
"tags": []
@@ -286,10 +286,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.037749,
- "end_time": "2020-08-05T07:33:38.658314",
+ "duration": 0.03551,
+ "end_time": "2020-08-06T07:32:30.593640",
"exception": false,
- "start_time": "2020-08-05T07:33:38.620565",
+ "start_time": "2020-08-06T07:32:30.558130",
"status": "completed"
},
"tags": []
@@ -308,10 +308,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.326858,
- "end_time": "2020-08-05T07:33:38.997546",
+ "duration": 0.339374,
+ "end_time": "2020-08-06T07:32:30.944934",
"exception": false,
- "start_time": "2020-08-05T07:33:38.670688",
+ "start_time": "2020-08-06T07:32:30.605560",
"status": "completed"
},
"tags": []
@@ -321,7 +321,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "8529 data points\n"
+ "8585 data points\n"
]
},
{
@@ -371,21 +371,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200804</td>\n",
+ " <td>20200805</td>\n",
" <td>AK</td>\n",
- " <td>4125.0</td>\n",
- " <td>248524.0</td>\n",
+ " <td>4183.0</td>\n",
+ " <td>253096.0</td>\n",
" <td>NaN</td>\n",
- " <td>33.0</td>\n",
+ " <td>38.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>...</td>\n",
- " <td>252649</td>\n",
+ " <td>257279</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
- " <td>59a8cabc3e35a5d51323bff0c43feacfd0806dc2</td>\n",
+ " <td>0a85599b284b6519c9ef59c495ee7e02bb9160a5</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>20200804</td>\n",
+ " <td>20200805</td>\n",
" <td>AL</td>\n",
- " <td>93702.0</td>\n",
- " <td>628599.0</td>\n",
+ " <td>94654.0</td>\n",
+ " <td>632806.0</td>\n",
" <td>NaN</td>\n",
- " <td>1517.0</td>\n",
+ " <td>1575.0</td>\n",
" <td>11100.0</td>\n",
" <td>NaN</td>\n",
- " <td>1173.0</td>\n",
+ " <td>1200.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>722301</td>\n",
- " <td>33</td>\n",
- " <td>235</td>\n",
- " <td>000ce6dde752f7fbcd8a4262d549da464dfabb5c</td>\n",
+ " <td>727460</td>\n",
+ " <td>29</td>\n",
+ " <td>0</td>\n",
+ " <td>672da264092f08c418d1945dcb919436e9d82d2f</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 20200804 AK 4125.0 248524.0 NaN 33.0 \n",
- "1 20200804 AL 93702.0 628599.0 NaN 1517.0 \n",
+ "0 20200805 AK 4183.0 253096.0 NaN 38.0 \n",
+ "1 20200805 AL 94654.0 632806.0 NaN 1575.0 \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 11100.0 NaN 1173.0 \n",
+ "1 11100.0 NaN 1200.0 \n",
"\n",
" onVentilatorCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 2.0 ... 252649 0 0 \n",
- "1 NaN ... 722301 33 235 \n",
+ "0 2.0 ... 257279 0 0 \n",
+ "1 NaN ... 727460 29 0 \n",
"\n",
" hash commercialScore \\\n",
- "0 59a8cabc3e35a5d51323bff0c43feacfd0806dc2 0 \n",
- "1 000ce6dde752f7fbcd8a4262d549da464dfabb5c 0 \n",
+ "0 0a85599b284b6519c9ef59c495ee7e02bb9160a5 0 \n",
+ "1 672da264092f08c418d1945dcb919436e9d82d2f 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": 6.958997,
- "end_time": "2020-08-05T07:33:39.426894",
+ "duration": 7.007186,
+ "end_time": "2020-08-06T07:32:31.268636",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/ooj1q6z_/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/y8yxp7e2/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/ooj1q6z_/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/y8yxp7e2/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-08-05T07:33:32.467897",
+ "start_time": "2020-08-06T07:32:24.261450",
"version": "1.1.0"
}
},
--
GitLab