From 5ee887179c9c93ae39021de274fe6d7937a21b41 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Sat, 22 Aug 2020 07:34:08 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../0ba04f702cfa491f882f048019edcf21.cwl | 120 ++++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 120 +++++++++---------
4 files changed, 184 insertions(+), 64 deletions(-)
create mode 100644 .renku/workflow/0ba04f702cfa491f882f048019edcf21.cwl
diff --git a/.renku/workflow/0ba04f702cfa491f882f048019edcf21.cwl b/.renku/workflow/0ba04f702cfa491f882f048019edcf21.cwl
new file mode 100644
index 000000000..7e14695a0
--- /dev/null
+++ b/.renku/workflow/0ba04f702cfa491f882f048019edcf21.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_1:
+ 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_0
+ - output_1
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index d490d4556..b07b10e7d 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 sha256:849a16fcd42d24e7cec4c16a40fbdc659a40e05bc8a32e7b781577b797568669
-size 12244691
+oid sha256:42d53de934f6e31aa5c593040183a14e0402e1f2e40bd12f701442a38a17ae63
+size 12317971
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 64e394a03..3d5219f68 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 sha256:5e5dcc7e8f24eb6ab8d056ee709db1335055c6fcc244b42eb60081d058d1ef33
-size 61501
+oid sha256:4f08c474017f1c9ac69a303ecf8a65d6e0c0c5e90aa3558de6de529fe1ec4b7a
+size 61806
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 1ec091fdb..09784b7b8 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": 3.222805,
- "end_time": "2020-08-21T07:35:01.009887",
+ "duration": 1.728575,
+ "end_time": "2020-08-22T07:34:05.577792",
"exception": false,
- "start_time": "2020-08-21T07:34:57.787082",
+ "start_time": "2020-08-22T07:34:03.849217",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.019356,
- "end_time": "2020-08-21T07:35:01.044072",
+ "duration": 0.022809,
+ "end_time": "2020-08-22T07:34:05.608763",
"exception": false,
- "start_time": "2020-08-21T07:35:01.024716",
+ "start_time": "2020-08-22T07:34:05.585954",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.018659,
- "end_time": "2020-08-21T07:35:01.070483",
+ "duration": 0.019005,
+ "end_time": "2020-08-22T07:34:05.635659",
"exception": false,
- "start_time": "2020-08-21T07:35:01.051824",
+ "start_time": "2020-08-22T07:34:05.616654",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/_pr6sx_7/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/n3gpc8oq/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": 0.005523,
- "end_time": "2020-08-21T07:35:01.083805",
+ "duration": 0.006777,
+ "end_time": "2020-08-22T07:34:05.650031",
"exception": false,
- "start_time": "2020-08-21T07:35:01.078282",
+ "start_time": "2020-08-22T07:34:05.643254",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.482961,
- "end_time": "2020-08-21T07:35:01.572388",
+ "duration": 0.529298,
+ "end_time": "2020-08-22T07:34:06.185227",
"exception": false,
- "start_time": "2020-08-21T07:35:01.089427",
+ "start_time": "2020-08-22T07:34:05.655929",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.02893,
- "end_time": "2020-08-21T07:35:01.616672",
+ "duration": 0.022671,
+ "end_time": "2020-08-22T07:34:06.221453",
"exception": false,
- "start_time": "2020-08-21T07:35:01.587742",
+ "start_time": "2020-08-22T07:34:06.198782",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.084829,
- "end_time": "2020-08-21T07:35:01.714810",
+ "duration": 0.074705,
+ "end_time": "2020-08-22T07:34:06.304356",
"exception": false,
- "start_time": "2020-08-21T07:35:01.629981",
+ "start_time": "2020-08-22T07:34:06.229651",
"status": "completed"
},
"tags": []
@@ -249,10 +249,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007688,
- "end_time": "2020-08-21T07:35:01.734487",
+ "duration": 0.006432,
+ "end_time": "2020-08-22T07:34:06.318679",
"exception": false,
- "start_time": "2020-08-21T07:35:01.726799",
+ "start_time": "2020-08-22T07:34:06.312247",
"status": "completed"
},
"tags": []
@@ -266,10 +266,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.823102,
- "end_time": "2020-08-21T07:35:02.564427",
+ "duration": 0.484023,
+ "end_time": "2020-08-22T07:34:06.809198",
"exception": false,
- "start_time": "2020-08-21T07:35:01.741325",
+ "start_time": "2020-08-22T07:34:06.325175",
"status": "completed"
},
"tags": []
@@ -286,10 +286,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.045027,
- "end_time": "2020-08-21T07:35:02.627273",
+ "duration": 0.046446,
+ "end_time": "2020-08-22T07:34:06.872970",
"exception": false,
- "start_time": "2020-08-21T07:35:02.582246",
+ "start_time": "2020-08-22T07:34:06.826524",
"status": "completed"
},
"tags": []
@@ -308,10 +308,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.445915,
- "end_time": "2020-08-21T07:35:03.090420",
+ "duration": 0.515919,
+ "end_time": "2020-08-22T07:34:07.403326",
"exception": false,
- "start_time": "2020-08-21T07:35:02.644505",
+ "start_time": "2020-08-22T07:34:06.887407",
"status": "completed"
},
"tags": []
@@ -321,7 +321,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "9449 data points\n"
+ "9505 data points\n"
]
},
{
@@ -371,21 +371,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200820</td>\n",
+ " <td>20200821</td>\n",
" <td>AK</td>\n",
- " <td>5332.0</td>\n",
- " <td>307315.0</td>\n",
+ " <td>5403.0</td>\n",
+ " <td>316132.0</td>\n",
" <td>NaN</td>\n",
- " <td>51.0</td>\n",
+ " <td>46.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>6.0</td>\n",
" <td>...</td>\n",
- " <td>312647</td>\n",
- " <td>0</td>\n",
+ " <td>321535</td>\n",
+ " <td>1</td>\n",
" <td>0</td>\n",
- " <td>c83a1d575a597788adccbe170950b8d197754b98</td>\n",
+ " <td>ac97da2a3705756521d2ad109926d4e477195879</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>20200820</td>\n",
+ " <td>20200821</td>\n",
" <td>AL</td>\n",
- " <td>112449.0</td>\n",
+ " <td>112770.0</td>\n",
" <td>784330.0</td>\n",
" <td>NaN</td>\n",
- " <td>1105.0</td>\n",
+ " <td>1168.0</td>\n",
" <td>13330.0</td>\n",
" <td>NaN</td>\n",
" <td>1348.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>896779</td>\n",
- " <td>30</td>\n",
- " <td>250</td>\n",
- " <td>39ccb36041e82b18489850d81c9e513b0c429e56</td>\n",
+ " <td>897100</td>\n",
+ " <td>16</td>\n",
+ " <td>0</td>\n",
+ " <td>7d05c9893cc3fff06668cf52e6806a369e1f5b63</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 20200820 AK 5332.0 307315.0 NaN 51.0 \n",
- "1 20200820 AL 112449.0 784330.0 NaN 1105.0 \n",
+ "0 20200821 AK 5403.0 316132.0 NaN 46.0 \n",
+ "1 20200821 AL 112770.0 784330.0 NaN 1168.0 \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
"1 13330.0 NaN 1348.0 \n",
"\n",
" onVentilatorCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 6.0 ... 312647 0 0 \n",
- "1 NaN ... 896779 30 250 \n",
+ "0 6.0 ... 321535 1 0 \n",
+ "1 NaN ... 897100 16 0 \n",
"\n",
" hash commercialScore \\\n",
- "0 c83a1d575a597788adccbe170950b8d197754b98 0 \n",
- "1 39ccb36041e82b18489850d81c9e513b0c429e56 0 \n",
+ "0 ac97da2a3705756521d2ad109926d4e477195879 0 \n",
+ "1 7d05c9893cc3fff06668cf52e6806a369e1f5b63 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": 7.62114,
- "end_time": "2020-08-21T07:35:03.526308",
+ "duration": 5.136938,
+ "end_time": "2020-08-22T07:34:07.836795",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/_pr6sx_7/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/n3gpc8oq/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/_pr6sx_7/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/n3gpc8oq/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-08-21T07:34:55.905168",
+ "start_time": "2020-08-22T07:34:02.699857",
"version": "1.1.0"
}
},
--
GitLab