From 91ecd5ac3db8a27216d4d47bb333022b1e487de1 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Sun, 6 Dec 2020 07:36:46 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../1a6aade63cae4283bb644ed4a14adec0.cwl | 120 ++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 136 +++++++++---------
4 files changed, 192 insertions(+), 72 deletions(-)
create mode 100644 .renku/workflow/1a6aade63cae4283bb644ed4a14adec0.cwl
diff --git a/.renku/workflow/1a6aade63cae4283bb644ed4a14adec0.cwl b/.renku/workflow/1a6aade63cae4283bb644ed4a14adec0.cwl
new file mode 100644
index 000000000..d2f1ef920
--- /dev/null
+++ b/.renku/workflow/1a6aade63cae4283bb644ed4a14adec0.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_0
+ streamable: false
+ type: File
+ output_3:
+ outputSource: step_3/output_1
+ streamable: false
+ type: Directory
+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 cedfaaa2c..87afbffbe 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:dc1388d54417d825e2fb7d5ac1438d69fc36f8836e13dbb98038fb24f595d243
-size 21181010
+oid sha256:a3628828503580ed48823aa574369330b240f7b22a454de93d09f818461ce7ed
+size 21258293
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index d6b9e29f2..1e43dae89 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:c776456ecf4648944100da79a2131cf140d61c21b2dea66a2cd6a26538a76e69
-size 145428
+oid sha256:8bcfdaa5409e4f9953474c5f60a032653b52d65518107a94d77b82bb2eb334ff
+size 146254
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index ce8912d37..2d191c18c 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": 5.263478,
- "end_time": "2020-12-05T07:37:55.779511",
+ "duration": 4.717714,
+ "end_time": "2020-12-06T07:36:42.848851",
"exception": false,
- "start_time": "2020-12-05T07:37:50.516033",
+ "start_time": "2020-12-06T07:36:38.131137",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.020627,
- "end_time": "2020-12-05T07:37:55.813877",
+ "duration": 0.020975,
+ "end_time": "2020-12-06T07:36:42.884296",
"exception": false,
- "start_time": "2020-12-05T07:37:55.793250",
+ "start_time": "2020-12-06T07:36:42.863321",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.017599,
- "end_time": "2020-12-05T07:37:55.839126",
+ "duration": 0.018155,
+ "end_time": "2020-12-06T07:36:42.910185",
"exception": false,
- "start_time": "2020-12-05T07:37:55.821527",
+ "start_time": "2020-12-06T07:36:42.892030",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/79vbklhn/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/bgj85y8_/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": 0.006687,
- "end_time": "2020-12-05T07:37:55.851844",
+ "duration": 0.005918,
+ "end_time": "2020-12-06T07:36:42.922347",
"exception": false,
- "start_time": "2020-12-05T07:37:55.845157",
+ "start_time": "2020-12-06T07:36:42.916429",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.75978,
- "end_time": "2020-12-05T07:37:56.616186",
+ "duration": 0.836113,
+ "end_time": "2020-12-06T07:36:43.763079",
"exception": false,
- "start_time": "2020-12-05T07:37:55.856406",
+ "start_time": "2020-12-06T07:36:42.926966",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.025756,
- "end_time": "2020-12-05T07:37:56.656315",
+ "duration": 0.022803,
+ "end_time": "2020-12-06T07:36:43.797693",
"exception": false,
- "start_time": "2020-12-05T07:37:56.630559",
+ "start_time": "2020-12-06T07:36:43.774890",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.071889,
- "end_time": "2020-12-05T07:37:56.742038",
+ "duration": 0.104921,
+ "end_time": "2020-12-06T07:36:43.911415",
"exception": false,
- "start_time": "2020-12-05T07:37:56.670149",
+ "start_time": "2020-12-06T07:36:43.806494",
"status": "completed"
},
"tags": []
@@ -284,10 +284,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008185,
- "end_time": "2020-12-05T07:37:56.763734",
+ "duration": 0.007727,
+ "end_time": "2020-12-06T07:36:43.931182",
"exception": false,
- "start_time": "2020-12-05T07:37:56.755549",
+ "start_time": "2020-12-06T07:36:43.923455",
"status": "completed"
},
"tags": []
@@ -301,10 +301,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.73386,
- "end_time": "2020-12-05T07:37:57.504423",
+ "duration": 0.674744,
+ "end_time": "2020-12-06T07:36:44.611412",
"exception": false,
- "start_time": "2020-12-05T07:37:56.770563",
+ "start_time": "2020-12-06T07:36:43.936668",
"status": "completed"
},
"tags": []
@@ -321,10 +321,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.054547,
- "end_time": "2020-12-05T07:37:57.575272",
+ "duration": 0.043869,
+ "end_time": "2020-12-06T07:36:44.670424",
"exception": false,
- "start_time": "2020-12-05T07:37:57.520725",
+ "start_time": "2020-12-06T07:36:44.626555",
"status": "completed"
},
"tags": []
@@ -343,10 +343,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.567192,
- "end_time": "2020-12-05T07:37:58.157210",
+ "duration": 0.584751,
+ "end_time": "2020-12-06T07:36:45.268667",
"exception": false,
- "start_time": "2020-12-05T07:37:57.590018",
+ "start_time": "2020-12-06T07:36:44.683916",
"status": "completed"
},
"tags": []
@@ -356,7 +356,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "15521 data points\n"
+ "15577 data points\n"
]
},
{
@@ -406,21 +406,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201204</td>\n",
+ " <td>20201205</td>\n",
" <td>AK</td>\n",
- " <td>34041.0</td>\n",
+ " <td>34963.0</td>\n",
" <td>NaN</td>\n",
- " <td>1016328.0</td>\n",
+ " <td>1032268.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1050369.0</td>\n",
- " <td>151.0</td>\n",
- " <td>794.0</td>\n",
+ " <td>1067231.0</td>\n",
+ " <td>166.0</td>\n",
+ " <td>799.0</td>\n",
" <td>...</td>\n",
- " <td>1050369</td>\n",
- " <td>12</td>\n",
- " <td>11</td>\n",
- " <td>e26ffb8603f9420d79be27ffffa4aff3ba2b2c2d</td>\n",
+ " <td>1067231</td>\n",
+ " <td>1</td>\n",
+ " <td>5</td>\n",
+ " <td>d8b27967afb185d8e4f38f5209d713ef23065d88</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -430,21 +430,21 @@
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20201204</td>\n",
+ " <td>20201205</td>\n",
" <td>AL</td>\n",
- " <td>264199.0</td>\n",
- " <td>45130.0</td>\n",
- " <td>1407299.0</td>\n",
+ " <td>267589.0</td>\n",
+ " <td>45785.0</td>\n",
+ " <td>1415357.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsPeopleViral</td>\n",
- " <td>1626368.0</td>\n",
- " <td>1875.0</td>\n",
+ " <td>1637161.0</td>\n",
+ " <td>1867.0</td>\n",
" <td>26331.0</td>\n",
" <td>...</td>\n",
- " <td>1671498</td>\n",
- " <td>55</td>\n",
- " <td>269</td>\n",
- " <td>fe8f40ae073982f6fce809ac9ed23bc3170f69e8</td>\n",
+ " <td>1682946</td>\n",
+ " <td>46</td>\n",
+ " <td>0</td>\n",
+ " <td>7a521812788c45e903b5a08f357bdd78f668340a</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -459,20 +459,20 @@
],
"text/plain": [
" date state positive probableCases negative pending \\\n",
- "0 20201204 AK 34041.0 NaN 1016328.0 NaN \n",
- "1 20201204 AL 264199.0 45130.0 1407299.0 NaN \n",
+ "0 20201205 AK 34963.0 NaN 1032268.0 NaN \n",
+ "1 20201205 AL 267589.0 45785.0 1415357.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 1050369.0 151.0 \n",
- "1 totalTestsPeopleViral 1626368.0 1875.0 \n",
+ "0 totalTestsViral 1067231.0 166.0 \n",
+ "1 totalTestsPeopleViral 1637161.0 1867.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 794.0 ... 1050369 12 11 \n",
- "1 26331.0 ... 1671498 55 269 \n",
+ "0 799.0 ... 1067231 1 5 \n",
+ "1 26331.0 ... 1682946 46 0 \n",
"\n",
" hash commercialScore \\\n",
- "0 e26ffb8603f9420d79be27ffffa4aff3ba2b2c2d 0 \n",
- "1 fe8f40ae073982f6fce809ac9ed23bc3170f69e8 0 \n",
+ "0 d8b27967afb185d8e4f38f5209d713ef23065d88 0 \n",
+ "1 7a521812788c45e903b5a08f357bdd78f668340a 0 \n",
"\n",
" negativeRegularScore negativeScore positiveScore score grade \n",
"0 0 0 0 0 \n",
@@ -512,18 +512,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 9.691808,
- "end_time": "2020-12-05T07:37:58.480279",
+ "duration": 9.124953,
+ "end_time": "2020-12-06T07:36:45.590793",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/79vbklhn/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/bgj85y8_/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/79vbklhn/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/bgj85y8_/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-12-05T07:37:48.788471",
+ "start_time": "2020-12-06T07:36:36.465840",
"version": "1.1.0"
}
},
--
GitLab