From 925135e1ea99555cf595046ca934059444146d19 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Mon, 7 Dec 2020 07:37:58 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../d960da088bd94329ae5215b9d22ad8d8.cwl | 120 ++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 132 +++++++++---------
4 files changed, 190 insertions(+), 70 deletions(-)
create mode 100644 .renku/workflow/d960da088bd94329ae5215b9d22ad8d8.cwl
diff --git a/.renku/workflow/d960da088bd94329ae5215b9d22ad8d8.cwl b/.renku/workflow/d960da088bd94329ae5215b9d22ad8d8.cwl
new file mode 100644
index 000000000..e4b2b04ae
--- /dev/null
+++ b/.renku/workflow/d960da088bd94329ae5215b9d22ad8d8.cwl
@@ -0,0 +1,120 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: out_folder
+ streamable: false
+ type: string
+ input_2:
+ default: data/covidtracking
+ streamable: false
+ type: string
+ input_3:
+ default:
+ class: File
+ path: ../../notebooks/process/download-covidtracking-data.ipynb
+ streamable: false
+ type: File
+ input_4:
+ default: runs/download-covidtracking-data.runs.ipynb
+ streamable: false
+ type: string
+ input_5:
+ default: states-daily.json
+ streamable: false
+ type: string
+ input_6:
+ default: states-metadata.json
+ streamable: false
+ type: string
+outputs:
+ output_2:
+ outputSource: step_1/output_0
+ streamable: false
+ type: File
+ output_3:
+ outputSource: step_1/output_1
+ streamable: false
+ type: Directory
+requirements: []
+steps:
+ step_1:
+ in:
+ input_1: input_1
+ input_2: input_2
+ input_3: input_3
+ input_4: input_4
+ out:
+ - output_1
+ - output_0
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
+ step_2:
+ in:
+ filename: input_5
+ input_directory: step_1/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_3:
+ in:
+ filename: input_6
+ input_directory: step_1/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: []
diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index 87afbffbe..6166bccda 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:a3628828503580ed48823aa574369330b240f7b22a454de93d09f818461ce7ed
-size 21258293
+oid sha256:1ca31123bba8b2cb17227b07d08312094fa1fdeb67294266da73e6fc4813e115
+size 21335523
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 1e43dae89..76b115006 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 sha256:8bcfdaa5409e4f9953474c5f60a032653b52d65518107a94d77b82bb2eb334ff
-size 146254
+oid sha256:a53136aa9dcd2c2aa2979195f39d9f5c0e68742b4abdaad373c519dc2337545c
+size 146464
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 2d191c18c..3bc594c00 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": 4.717714,
- "end_time": "2020-12-06T07:36:42.848851",
+ "duration": 4.152565,
+ "end_time": "2020-12-07T07:37:54.515472",
"exception": false,
- "start_time": "2020-12-06T07:36:38.131137",
+ "start_time": "2020-12-07T07:37:50.362907",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.020975,
- "end_time": "2020-12-06T07:36:42.884296",
+ "duration": 0.020423,
+ "end_time": "2020-12-07T07:37:54.550390",
"exception": false,
- "start_time": "2020-12-06T07:36:42.863321",
+ "start_time": "2020-12-07T07:37:54.529967",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.018155,
- "end_time": "2020-12-06T07:36:42.910185",
+ "duration": 0.018496,
+ "end_time": "2020-12-07T07:37:54.576647",
"exception": false,
- "start_time": "2020-12-06T07:36:42.892030",
+ "start_time": "2020-12-07T07:37:54.558151",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/bgj85y8_/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/x6h2bjc3/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": 0.005918,
- "end_time": "2020-12-06T07:36:42.922347",
+ "duration": 0.006579,
+ "end_time": "2020-12-07T07:37:54.590047",
"exception": false,
- "start_time": "2020-12-06T07:36:42.916429",
+ "start_time": "2020-12-07T07:37:54.583468",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.836113,
- "end_time": "2020-12-06T07:36:43.763079",
+ "duration": 0.69645,
+ "end_time": "2020-12-07T07:37:55.291679",
"exception": false,
- "start_time": "2020-12-06T07:36:42.926966",
+ "start_time": "2020-12-07T07:37:54.595229",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.022803,
- "end_time": "2020-12-06T07:36:43.797693",
+ "duration": 0.022024,
+ "end_time": "2020-12-07T07:37:55.325785",
"exception": false,
- "start_time": "2020-12-06T07:36:43.774890",
+ "start_time": "2020-12-07T07:37:55.303761",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.104921,
- "end_time": "2020-12-06T07:36:43.911415",
+ "duration": 0.069775,
+ "end_time": "2020-12-07T07:37:55.403880",
"exception": false,
- "start_time": "2020-12-06T07:36:43.806494",
+ "start_time": "2020-12-07T07:37:55.334105",
"status": "completed"
},
"tags": []
@@ -284,10 +284,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007727,
- "end_time": "2020-12-06T07:36:43.931182",
+ "duration": 0.007851,
+ "end_time": "2020-12-07T07:37:55.425086",
"exception": false,
- "start_time": "2020-12-06T07:36:43.923455",
+ "start_time": "2020-12-07T07:37:55.417235",
"status": "completed"
},
"tags": []
@@ -301,10 +301,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.674744,
- "end_time": "2020-12-06T07:36:44.611412",
+ "duration": 0.741031,
+ "end_time": "2020-12-07T07:37:56.172694",
"exception": false,
- "start_time": "2020-12-06T07:36:43.936668",
+ "start_time": "2020-12-07T07:37:55.431663",
"status": "completed"
},
"tags": []
@@ -321,10 +321,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.043869,
- "end_time": "2020-12-06T07:36:44.670424",
+ "duration": 0.0364,
+ "end_time": "2020-12-07T07:37:56.223660",
"exception": false,
- "start_time": "2020-12-06T07:36:44.626555",
+ "start_time": "2020-12-07T07:37:56.187260",
"status": "completed"
},
"tags": []
@@ -343,10 +343,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.584751,
- "end_time": "2020-12-06T07:36:45.268667",
+ "duration": 0.475217,
+ "end_time": "2020-12-07T07:37:56.707381",
"exception": false,
- "start_time": "2020-12-06T07:36:44.683916",
+ "start_time": "2020-12-07T07:37:56.232164",
"status": "completed"
},
"tags": []
@@ -356,7 +356,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "15577 data points\n"
+ "15633 data points\n"
]
},
{
@@ -406,21 +406,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201205</td>\n",
+ " <td>20201206</td>\n",
" <td>AK</td>\n",
- " <td>34963.0</td>\n",
+ " <td>35720.0</td>\n",
" <td>NaN</td>\n",
- " <td>1032268.0</td>\n",
+ " <td>1042056.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1067231.0</td>\n",
- " <td>166.0</td>\n",
+ " <td>1077776.0</td>\n",
+ " <td>164.0</td>\n",
" <td>799.0</td>\n",
" <td>...</td>\n",
- " <td>1067231</td>\n",
- " <td>1</td>\n",
- " <td>5</td>\n",
- " <td>d8b27967afb185d8e4f38f5209d713ef23065d88</td>\n",
+ " <td>1077776</td>\n",
+ " <td>0</td>\n",
+ " <td>0</td>\n",
+ " <td>7b1d31e2756687bb9259b29195f1db6cdb321ea6</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>20201205</td>\n",
+ " <td>20201206</td>\n",
" <td>AL</td>\n",
- " <td>267589.0</td>\n",
- " <td>45785.0</td>\n",
- " <td>1415357.0</td>\n",
+ " <td>269877.0</td>\n",
+ " <td>45962.0</td>\n",
+ " <td>1421126.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsPeopleViral</td>\n",
- " <td>1637161.0</td>\n",
- " <td>1867.0</td>\n",
+ " <td>1645041.0</td>\n",
+ " <td>1927.0</td>\n",
" <td>26331.0</td>\n",
" <td>...</td>\n",
- " <td>1682946</td>\n",
- " <td>46</td>\n",
+ " <td>1691003</td>\n",
+ " <td>12</td>\n",
" <td>0</td>\n",
- " <td>7a521812788c45e903b5a08f357bdd78f668340a</td>\n",
+ " <td>19454ed8fe28fc0a7948fc0771b2f3c846c1c92e</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 20201205 AK 34963.0 NaN 1032268.0 NaN \n",
- "1 20201205 AL 267589.0 45785.0 1415357.0 NaN \n",
+ "0 20201206 AK 35720.0 NaN 1042056.0 NaN \n",
+ "1 20201206 AL 269877.0 45962.0 1421126.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 1067231.0 166.0 \n",
- "1 totalTestsPeopleViral 1637161.0 1867.0 \n",
+ "0 totalTestsViral 1077776.0 164.0 \n",
+ "1 totalTestsPeopleViral 1645041.0 1927.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 799.0 ... 1067231 1 5 \n",
- "1 26331.0 ... 1682946 46 0 \n",
+ "0 799.0 ... 1077776 0 0 \n",
+ "1 26331.0 ... 1691003 12 0 \n",
"\n",
" hash commercialScore \\\n",
- "0 d8b27967afb185d8e4f38f5209d713ef23065d88 0 \n",
- "1 7a521812788c45e903b5a08f357bdd78f668340a 0 \n",
+ "0 7b1d31e2756687bb9259b29195f1db6cdb321ea6 0 \n",
+ "1 19454ed8fe28fc0a7948fc0771b2f3c846c1c92e 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": 9.124953,
- "end_time": "2020-12-06T07:36:45.590793",
+ "duration": 8.764442,
+ "end_time": "2020-12-07T07:37:57.030694",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/bgj85y8_/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/x6h2bjc3/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/bgj85y8_/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/x6h2bjc3/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-12-06T07:36:36.465840",
+ "start_time": "2020-12-07T07:37:48.266252",
"version": "1.1.0"
}
},
--
GitLab