From 4597cd96a8c52ccc007d7402321877b4e9bf9a01 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Fri, 5 Jun 2020 07:26:42 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../faf9a75a6e43415bb1c5b9b002e51f78.cwl | 120 +++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 126 +++++++++---------
4 files changed, 187 insertions(+), 67 deletions(-)
create mode 100644 .renku/workflow/faf9a75a6e43415bb1c5b9b002e51f78.cwl
diff --git a/.renku/workflow/faf9a75a6e43415bb1c5b9b002e51f78.cwl b/.renku/workflow/faf9a75a6e43415bb1c5b9b002e51f78.cwl
new file mode 100644
index 000000000..0c4ffa04b
--- /dev/null
+++ b/.renku/workflow/faf9a75a6e43415bb1c5b9b002e51f78.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: states-daily.json
+ streamable: false
+ type: string
+ input_3:
+ default: out_folder
+ streamable: false
+ type: string
+ input_4:
+ default: data/covidtracking
+ streamable: false
+ type: string
+ input_5:
+ default:
+ class: File
+ path: ../../notebooks/process/download-covidtracking-data.ipynb
+ streamable: false
+ type: File
+ input_6:
+ default: runs/download-covidtracking-data.runs.ipynb
+ streamable: false
+ type: string
+outputs:
+ output_0:
+ outputSource: step_3/output_1
+ streamable: false
+ type: Directory
+ output_2:
+ outputSource: step_3/output_0
+ streamable: false
+ type: File
+requirements: []
+steps:
+ step_1:
+ in:
+ filename: input_1
+ input_directory: step_3/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:
+ filename: input_2
+ input_directory: step_3/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: []
+ step_3:
+ in:
+ input_1: input_3
+ input_2: input_4
+ input_3: input_5
+ input_4: input_6
+ out:
+ - output_1
+ - output_0
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index 1f039ac48..3c4b186a3 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 sha256:8cd217cca3afcedb310e36a7ea42508c92271044acc349992bea5abf79a05f6a
-size 3940450
+oid sha256:3bd629062dd7df6fbfecb645e2597200da55a411b07f8a3b946a125e47da60a8
+size 3984683
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 28ce6ebec..c1e746486 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 sha256:8b0c5cfa8aedded7e57c76535faaa4f2b863b26d50909e984a39bbf6e8a5de59
-size 34797
+oid sha256:c7ab8c45e4de35bc9cf318cf88bc92f858170281fc558ef94f15b0c471e084b2
+size 35112
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 07cba5714..008a705b3 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": 4.627897,
- "end_time": "2020-06-04T08:28:04.985732",
+ "duration": 1.081365,
+ "end_time": "2020-06-05T07:26:40.376216",
"exception": false,
- "start_time": "2020-06-04T08:28:00.357835",
+ "start_time": "2020-06-05T07:26:39.294851",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.022291,
- "end_time": "2020-06-04T08:28:05.020399",
+ "duration": 0.026604,
+ "end_time": "2020-06-05T07:26:40.419396",
"exception": false,
- "start_time": "2020-06-04T08:28:04.998108",
+ "start_time": "2020-06-05T07:26:40.392792",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.022545,
- "end_time": "2020-06-04T08:28:05.052282",
+ "duration": 0.023283,
+ "end_time": "2020-06-05T07:26:40.455880",
"exception": false,
- "start_time": "2020-06-04T08:28:05.029737",
+ "start_time": "2020-06-05T07:26:40.432597",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/m_83rm_4/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/nhlov4s_/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": 0.007006,
- "end_time": "2020-06-04T08:28:05.068409",
+ "duration": 0.007144,
+ "end_time": "2020-06-05T07:26:40.473105",
"exception": false,
- "start_time": "2020-06-04T08:28:05.061403",
+ "start_time": "2020-06-05T07:26:40.465961",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.381514,
- "end_time": "2020-06-04T08:28:05.457090",
+ "duration": 0.174501,
+ "end_time": "2020-06-05T07:26:40.653764",
"exception": false,
- "start_time": "2020-06-04T08:28:05.075576",
+ "start_time": "2020-06-05T07:26:40.479263",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.027088,
- "end_time": "2020-06-04T08:28:05.496958",
+ "duration": 0.025897,
+ "end_time": "2020-06-05T07:26:40.695095",
"exception": false,
- "start_time": "2020-06-04T08:28:05.469870",
+ "start_time": "2020-06-05T07:26:40.669198",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.072587,
- "end_time": "2020-06-04T08:28:05.580434",
+ "duration": 0.073474,
+ "end_time": "2020-06-05T07:26:40.778005",
"exception": false,
- "start_time": "2020-06-04T08:28:05.507847",
+ "start_time": "2020-06-05T07:26:40.704531",
"status": "completed"
},
"tags": []
@@ -242,10 +242,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008248,
- "end_time": "2020-06-04T08:28:05.598828",
+ "duration": 0.00772,
+ "end_time": "2020-06-05T07:26:40.798117",
"exception": false,
- "start_time": "2020-06-04T08:28:05.590580",
+ "start_time": "2020-06-05T07:26:40.790397",
"status": "completed"
},
"tags": []
@@ -259,10 +259,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.154111,
- "end_time": "2020-06-04T08:28:05.761833",
+ "duration": 0.209878,
+ "end_time": "2020-06-05T07:26:41.014535",
"exception": false,
- "start_time": "2020-06-04T08:28:05.607722",
+ "start_time": "2020-06-05T07:26:40.804657",
"status": "completed"
},
"tags": []
@@ -279,10 +279,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.029699,
- "end_time": "2020-06-04T08:28:05.803127",
+ "duration": 0.033848,
+ "end_time": "2020-06-05T07:26:41.066030",
"exception": false,
- "start_time": "2020-06-04T08:28:05.773428",
+ "start_time": "2020-06-05T07:26:41.032182",
"status": "completed"
},
"tags": []
@@ -301,10 +301,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.20856,
- "end_time": "2020-06-04T08:28:06.022260",
+ "duration": 0.195065,
+ "end_time": "2020-06-05T07:26:41.272416",
"exception": false,
- "start_time": "2020-06-04T08:28:05.813700",
+ "start_time": "2020-06-05T07:26:41.077351",
"status": "completed"
},
"tags": []
@@ -314,7 +314,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "5057 data points\n"
+ "5113 data points\n"
]
},
{
@@ -364,21 +364,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200603</td>\n",
+ " <td>20200604</td>\n",
" <td>AK</td>\n",
- " <td>505.0</td>\n",
- " <td>57677.0</td>\n",
+ " <td>513.0</td>\n",
+ " <td>59584.0</td>\n",
" <td>NaN</td>\n",
- " <td>11.0</td>\n",
+ " <td>13.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>0.0</td>\n",
+ " <td>1.0</td>\n",
" <td>...</td>\n",
- " <td>58182</td>\n",
+ " <td>60097</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
- " <td>02548c93014e510ca02e0fc92122c299e4aa8e78</td>\n",
+ " <td>c1046011af7271cbe2e6698526714c6cb5b92748</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -388,21 +388,21 @@
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200603</td>\n",
+ " <td>20200604</td>\n",
" <td>AL</td>\n",
- " <td>18851.0</td>\n",
- " <td>212743.0</td>\n",
+ " <td>19072.0</td>\n",
+ " <td>216227.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>1900.0</td>\n",
+ " <td>1929.0</td>\n",
" <td>NaN</td>\n",
- " <td>591.0</td>\n",
+ " <td>601.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>231594</td>\n",
- " <td>2</td>\n",
- " <td>21</td>\n",
- " <td>fe5df10e9c8639e15d2ce02d16d678e16f6f6cc7</td>\n",
+ " <td>235299</td>\n",
+ " <td>0</td>\n",
+ " <td>29</td>\n",
+ " <td>bcbefdb36212ba2b97b5a354f4e45bf16648ee23</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -417,20 +417,20 @@
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200603 AK 505.0 57677.0 NaN 11.0 \n",
- "1 20200603 AL 18851.0 212743.0 NaN NaN \n",
+ "0 20200604 AK 513.0 59584.0 NaN 13.0 \n",
+ "1 20200604 AL 19072.0 216227.0 NaN NaN \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 1900.0 NaN 591.0 \n",
+ "1 1929.0 NaN 601.0 \n",
"\n",
" onVentilatorCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 0.0 ... 58182 0 0 \n",
- "1 NaN ... 231594 2 21 \n",
+ "0 1.0 ... 60097 0 0 \n",
+ "1 NaN ... 235299 0 29 \n",
"\n",
" hash commercialScore \\\n",
- "0 02548c93014e510ca02e0fc92122c299e4aa8e78 0 \n",
- "1 fe5df10e9c8639e15d2ce02d16d678e16f6f6cc7 0 \n",
+ "0 c1046011af7271cbe2e6698526714c6cb5b92748 0 \n",
+ "1 bcbefdb36212ba2b97b5a354f4e45bf16648ee23 0 \n",
"\n",
" negativeRegularScore negativeScore positiveScore score grade \n",
"0 0 0 0 0 \n",
@@ -470,18 +470,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 7.919109,
- "end_time": "2020-06-04T08:28:06.447225",
+ "duration": 3.349554,
+ "end_time": "2020-06-05T07:26:41.597056",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/m_83rm_4/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/nhlov4s_/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/m_83rm_4/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/nhlov4s_/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-06-04T08:27:58.528116",
+ "start_time": "2020-06-05T07:26:38.247502",
"version": "1.1.0"
}
},
--
GitLab