From dadaeaeca1cef285c48fd093c3c400c74bbae9d7 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Sun, 4 Oct 2020 07:37:11 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../f63b90cc031348a5b51119ee816c1fbb.cwl | 120 ++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 3 +
runs/download-covidtracking-data.runs.ipynb | 132 +++++++++---------
4 files changed, 191 insertions(+), 68 deletions(-)
create mode 100644 .renku/workflow/f63b90cc031348a5b51119ee816c1fbb.cwl
create mode 100644 data/covidtracking/states-metadata.json
diff --git a/.renku/workflow/f63b90cc031348a5b51119ee816c1fbb.cwl b/.renku/workflow/f63b90cc031348a5b51119ee816c1fbb.cwl
new file mode 100644
index 000000000..5083736b1
--- /dev/null
+++ b/.renku/workflow/f63b90cc031348a5b51119ee816c1fbb.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_1:
+ 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 d26ad32fd..bfd78f3b5 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 sha256:8ebad7d955d752aceb574fc1350ef6a762ee12ab5c260ab3c6dd4afec3d49f5c
-size 15885953
+oid sha256:fda93dc045f578a2c5e25eb3c983207c6ae65b98b4edd197d8d24cafcdf4dd9c
+size 15961292
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
new file mode 100644
index 000000000..0c501462c
--- /dev/null
+++ b/data/covidtracking/states-metadata.json
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:332734a3fad7b29d49cbc3275b1a653f2a41fb67abc9cb4916d4923e6c826ceb
+size 88234
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 9f40ab1cc..53ca290ba 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": 5.253052,
- "end_time": "2020-10-03T07:35:25.026066",
+ "duration": 2.806523,
+ "end_time": "2020-10-04T07:36:42.384725",
"exception": false,
- "start_time": "2020-10-03T07:35:19.773014",
+ "start_time": "2020-10-04T07:36:39.578202",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.022596,
- "end_time": "2020-10-03T07:35:25.064552",
+ "duration": 0.026644,
+ "end_time": "2020-10-04T07:36:42.427822",
"exception": false,
- "start_time": "2020-10-03T07:35:25.041956",
+ "start_time": "2020-10-04T07:36:42.401178",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.020122,
- "end_time": "2020-10-03T07:35:25.093667",
+ "duration": 0.027029,
+ "end_time": "2020-10-04T07:36:42.466206",
"exception": false,
- "start_time": "2020-10-03T07:35:25.073545",
+ "start_time": "2020-10-04T07:36:42.439177",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/zy0hkj0c/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/itdjbwep/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": 0.006778,
- "end_time": "2020-10-03T07:35:25.108259",
+ "duration": 0.007141,
+ "end_time": "2020-10-04T07:36:42.483750",
"exception": false,
- "start_time": "2020-10-03T07:35:25.101481",
+ "start_time": "2020-10-04T07:36:42.476609",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.532189,
- "end_time": "2020-10-03T07:35:25.645896",
+ "duration": 0.313267,
+ "end_time": "2020-10-04T07:36:42.803613",
"exception": false,
- "start_time": "2020-10-03T07:35:25.113707",
+ "start_time": "2020-10-04T07:36:42.490346",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.022618,
- "end_time": "2020-10-03T07:35:25.681256",
+ "duration": 0.030218,
+ "end_time": "2020-10-04T07:36:42.847821",
"exception": false,
- "start_time": "2020-10-03T07:35:25.658638",
+ "start_time": "2020-10-04T07:36:42.817603",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.091493,
- "end_time": "2020-10-03T07:35:25.780175",
+ "duration": 0.10747,
+ "end_time": "2020-10-04T07:36:42.963741",
"exception": false,
- "start_time": "2020-10-03T07:35:25.688682",
+ "start_time": "2020-10-04T07:36:42.856271",
"status": "completed"
},
"tags": []
@@ -280,10 +280,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.006967,
- "end_time": "2020-10-03T07:35:25.803168",
+ "duration": 0.008123,
+ "end_time": "2020-10-04T07:36:42.985675",
"exception": false,
- "start_time": "2020-10-03T07:35:25.796201",
+ "start_time": "2020-10-04T07:36:42.977552",
"status": "completed"
},
"tags": []
@@ -297,10 +297,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 26.252126,
- "end_time": "2020-10-03T07:35:52.061529",
+ "duration": 26.366353,
+ "end_time": "2020-10-04T07:37:09.358813",
"exception": false,
- "start_time": "2020-10-03T07:35:25.809403",
+ "start_time": "2020-10-04T07:36:42.992460",
"status": "completed"
},
"tags": []
@@ -317,10 +317,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.06406,
- "end_time": "2020-10-03T07:35:52.143430",
+ "duration": 0.05094,
+ "end_time": "2020-10-04T07:37:09.428545",
"exception": false,
- "start_time": "2020-10-03T07:35:52.079370",
+ "start_time": "2020-10-04T07:37:09.377605",
"status": "completed"
},
"tags": []
@@ -339,10 +339,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.575261,
- "end_time": "2020-10-03T07:35:52.733021",
+ "duration": 0.543571,
+ "end_time": "2020-10-04T07:37:09.990596",
"exception": false,
- "start_time": "2020-10-03T07:35:52.157760",
+ "start_time": "2020-10-04T07:37:09.447025",
"status": "completed"
},
"tags": []
@@ -352,7 +352,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "11914 data points\n"
+ "11970 data points\n"
]
},
{
@@ -402,21 +402,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201002</td>\n",
+ " <td>20201003</td>\n",
" <td>AK</td>\n",
- " <td>9040.0</td>\n",
- " <td>460250.0</td>\n",
+ " <td>9187.0</td>\n",
+ " <td>464069.0</td>\n",
" <td>NaN</td>\n",
- " <td>469290.0</td>\n",
- " <td>41.0</td>\n",
+ " <td>473256.0</td>\n",
+ " <td>39.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>469290</td>\n",
- " <td>0</td>\n",
+ " <td>473256</td>\n",
+ " <td>1</td>\n",
" <td>0</td>\n",
- " <td>77ea689d232f21d7c3e86721a92703f37b818df6</td>\n",
+ " <td>be3501a43c9157686572d7e2a30834da4ae8a25a</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>20201002</td>\n",
+ " <td>20201003</td>\n",
" <td>AL</td>\n",
- " <td>156698.0</td>\n",
- " <td>1006612.0</td>\n",
+ " <td>158380.0</td>\n",
+ " <td>1016319.0</td>\n",
" <td>NaN</td>\n",
- " <td>1145601.0</td>\n",
- " <td>752.0</td>\n",
+ " <td>1156045.0</td>\n",
+ " <td>738.0</td>\n",
" <td>17420.0</td>\n",
" <td>NaN</td>\n",
- " <td>1840.0</td>\n",
+ " <td>1843.0</td>\n",
" <td>...</td>\n",
- " <td>1163310</td>\n",
- " <td>2</td>\n",
- " <td>163</td>\n",
- " <td>38da52ec54bc8d9114fc1ef392985f137e8c9e1f</td>\n",
+ " <td>1174699</td>\n",
+ " <td>8</td>\n",
+ " <td>0</td>\n",
+ " <td>38e00bf1704ab9fd7e05553420b27c9ab7b3cfed</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -455,20 +455,20 @@
],
"text/plain": [
" date state positive negative pending totalTestResults \\\n",
- "0 20201002 AK 9040.0 460250.0 NaN 469290.0 \n",
- "1 20201002 AL 156698.0 1006612.0 NaN 1145601.0 \n",
+ "0 20201003 AK 9187.0 464069.0 NaN 473256.0 \n",
+ "1 20201003 AL 158380.0 1016319.0 NaN 1156045.0 \n",
"\n",
" hospitalizedCurrently hospitalizedCumulative inIcuCurrently \\\n",
- "0 41.0 NaN NaN \n",
- "1 752.0 17420.0 NaN \n",
+ "0 39.0 NaN NaN \n",
+ "1 738.0 17420.0 NaN \n",
"\n",
" inIcuCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 NaN ... 469290 0 0 \n",
- "1 1840.0 ... 1163310 2 163 \n",
+ "0 NaN ... 473256 1 0 \n",
+ "1 1843.0 ... 1174699 8 0 \n",
"\n",
" hash commercialScore \\\n",
- "0 77ea689d232f21d7c3e86721a92703f37b818df6 0 \n",
- "1 38da52ec54bc8d9114fc1ef392985f137e8c9e1f 0 \n",
+ "0 be3501a43c9157686572d7e2a30834da4ae8a25a 0 \n",
+ "1 38e00bf1704ab9fd7e05553420b27c9ab7b3cfed 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": 36.095374,
- "end_time": "2020-10-03T07:35:53.164442",
+ "duration": 32.638534,
+ "end_time": "2020-10-04T07:37:10.419011",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/zy0hkj0c/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/itdjbwep/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/zy0hkj0c/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/itdjbwep/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-10-03T07:35:17.069068",
+ "start_time": "2020-10-04T07:36:37.780477",
"version": "1.1.0"
}
},
--
GitLab