From 925756b69c27cff7df779633d5b0598a086784e3 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Wed, 16 Sep 2020 07:35:51 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../ed22b9067a714a60aa63af2ba94b8a5d.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/ed22b9067a714a60aa63af2ba94b8a5d.cwl
diff --git a/.renku/workflow/ed22b9067a714a60aa63af2ba94b8a5d.cwl b/.renku/workflow/ed22b9067a714a60aa63af2ba94b8a5d.cwl
new file mode 100644
index 000000000..e5710c831
--- /dev/null
+++ b/.renku/workflow/ed22b9067a714a60aa63af2ba94b8a5d.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: states-metadata.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_3:
+ 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-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:
+ 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-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: []
+ 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 48da09c3c..2543d2dfd 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 sha256:6136c9676e800850762ab1152701a61382c92f61980841d108c11146a29bd9b1
-size 14530788
+oid sha256:89f20e92c5fb87d687ea74d5cdbb8e92e6a10c099199bbe4c21dc2b6d83ec9ff
+size 14606134
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 271a33c1d..cf376b61d 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 sha256:99b0108722e9576f5d6a8d806819357999bb461cbc13f575db5c366bfbba325d
-size 74414
+oid sha256:e220b9502811e769d29769330ed10ccda4981c9ee60ec1080bf538e82cd0f1e4
+size 75111
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 29dcbdf6d..f27824a6c 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": 3.758726,
- "end_time": "2020-09-15T07:34:48.490913",
+ "duration": 3.099848,
+ "end_time": "2020-09-16T07:35:23.188379",
"exception": false,
- "start_time": "2020-09-15T07:34:44.732187",
+ "start_time": "2020-09-16T07:35:20.088531",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.029344,
- "end_time": "2020-09-15T07:34:48.536522",
+ "duration": 0.029918,
+ "end_time": "2020-09-16T07:35:23.235828",
"exception": false,
- "start_time": "2020-09-15T07:34:48.507178",
+ "start_time": "2020-09-16T07:35:23.205910",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.033826,
- "end_time": "2020-09-15T07:34:48.580975",
+ "duration": 0.026953,
+ "end_time": "2020-09-16T07:35:23.278213",
"exception": false,
- "start_time": "2020-09-15T07:34:48.547149",
+ "start_time": "2020-09-16T07:35:23.251260",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/jsxpi5jx/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/ahwdc6db/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": 0.010067,
- "end_time": "2020-09-15T07:34:48.605607",
+ "duration": 0.008342,
+ "end_time": "2020-09-16T07:35:23.301372",
"exception": false,
- "start_time": "2020-09-15T07:34:48.595540",
+ "start_time": "2020-09-16T07:35:23.293030",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.82058,
- "end_time": "2020-09-15T07:34:49.433425",
+ "duration": 0.6195,
+ "end_time": "2020-09-16T07:35:23.928157",
"exception": false,
- "start_time": "2020-09-15T07:34:48.612845",
+ "start_time": "2020-09-16T07:35:23.308657",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.027218,
- "end_time": "2020-09-15T07:34:49.474403",
+ "duration": 0.0249,
+ "end_time": "2020-09-16T07:35:23.968133",
"exception": false,
- "start_time": "2020-09-15T07:34:49.447185",
+ "start_time": "2020-09-16T07:35:23.943233",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.094807,
- "end_time": "2020-09-15T07:34:49.578347",
+ "duration": 0.081013,
+ "end_time": "2020-09-16T07:35:24.057991",
"exception": false,
- "start_time": "2020-09-15T07:34:49.483540",
+ "start_time": "2020-09-16T07:35:23.976978",
"status": "completed"
},
"tags": []
@@ -263,10 +263,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007654,
- "end_time": "2020-09-15T07:34:49.599510",
+ "duration": 0.008085,
+ "end_time": "2020-09-16T07:35:24.081112",
"exception": false,
- "start_time": "2020-09-15T07:34:49.591856",
+ "start_time": "2020-09-16T07:35:24.073027",
"status": "completed"
},
"tags": []
@@ -280,10 +280,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 24.500853,
- "end_time": "2020-09-15T07:35:14.107416",
+ "duration": 25.020287,
+ "end_time": "2020-09-16T07:35:49.108196",
"exception": false,
- "start_time": "2020-09-15T07:34:49.606563",
+ "start_time": "2020-09-16T07:35:24.087909",
"status": "completed"
},
"tags": []
@@ -300,10 +300,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.052058,
- "end_time": "2020-09-15T07:35:14.175197",
+ "duration": 0.04623,
+ "end_time": "2020-09-16T07:35:49.168681",
"exception": false,
- "start_time": "2020-09-15T07:35:14.123139",
+ "start_time": "2020-09-16T07:35:49.122451",
"status": "completed"
},
"tags": []
@@ -322,10 +322,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.515353,
- "end_time": "2020-09-15T07:35:14.706843",
+ "duration": 0.566828,
+ "end_time": "2020-09-16T07:35:49.749325",
"exception": false,
- "start_time": "2020-09-15T07:35:14.191490",
+ "start_time": "2020-09-16T07:35:49.182497",
"status": "completed"
},
"tags": []
@@ -335,7 +335,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "10906 data points\n"
+ "10962 data points\n"
]
},
{
@@ -385,21 +385,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200914</td>\n",
+ " <td>20200915</td>\n",
" <td>AK</td>\n",
- " <td>7270.0</td>\n",
- " <td>396143.0</td>\n",
+ " <td>7313.0</td>\n",
+ " <td>399811.0</td>\n",
" <td>NaN</td>\n",
- " <td>37.0</td>\n",
+ " <td>44.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>8.0</td>\n",
" <td>...</td>\n",
- " <td>403413</td>\n",
+ " <td>407124</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
- " <td>c47ba6fdd7b2d5856a69b861c773b64ba0dfcb76</td>\n",
+ " <td>b7d286bbeacaeef7cbaed188fba49cfe43c44450</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -409,21 +409,21 @@
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200914</td>\n",
+ " <td>20200915</td>\n",
" <td>AL</td>\n",
- " <td>139459.0</td>\n",
- " <td>888092.0</td>\n",
+ " <td>140160.0</td>\n",
+ " <td>892810.0</td>\n",
" <td>NaN</td>\n",
- " <td>792.0</td>\n",
+ " <td>716.0</td>\n",
" <td>15756.0</td>\n",
" <td>NaN</td>\n",
- " <td>1611.0</td>\n",
+ " <td>1622.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>1027551</td>\n",
- " <td>4</td>\n",
- " <td>229</td>\n",
- " <td>a852a907f21a1d2ec711d522217d2fa536b912e5</td>\n",
+ " <td>1032970</td>\n",
+ " <td>32</td>\n",
+ " <td>0</td>\n",
+ " <td>0f70ad393cc6c32f0b4ea5e8269035c8c655cc6d</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -438,20 +438,20 @@
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200914 AK 7270.0 396143.0 NaN 37.0 \n",
- "1 20200914 AL 139459.0 888092.0 NaN 792.0 \n",
+ "0 20200915 AK 7313.0 399811.0 NaN 44.0 \n",
+ "1 20200915 AL 140160.0 892810.0 NaN 716.0 \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 15756.0 NaN 1611.0 \n",
+ "1 15756.0 NaN 1622.0 \n",
"\n",
" onVentilatorCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 8.0 ... 403413 0 0 \n",
- "1 NaN ... 1027551 4 229 \n",
+ "0 8.0 ... 407124 0 0 \n",
+ "1 NaN ... 1032970 32 0 \n",
"\n",
" hash commercialScore \\\n",
- "0 c47ba6fdd7b2d5856a69b861c773b64ba0dfcb76 0 \n",
- "1 a852a907f21a1d2ec711d522217d2fa536b912e5 0 \n",
+ "0 b7d286bbeacaeef7cbaed188fba49cfe43c44450 0 \n",
+ "1 0f70ad393cc6c32f0b4ea5e8269035c8c655cc6d 0 \n",
"\n",
" negativeRegularScore negativeScore positiveScore score grade \n",
"0 0 0 0 0 \n",
@@ -491,18 +491,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 32.417203,
- "end_time": "2020-09-15T07:35:15.138903",
+ "duration": 31.86503,
+ "end_time": "2020-09-16T07:35:50.171977",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/jsxpi5jx/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/ahwdc6db/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/jsxpi5jx/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/ahwdc6db/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-09-15T07:34:42.721700",
+ "start_time": "2020-09-16T07:35:18.306947",
"version": "1.1.0"
}
},
--
GitLab