From 5d46b5300156c2ec9aadb1660b69b19dcd20dcc8 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Thu, 10 Dec 2020 07:45:08 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../d38156548319433aa76d8a44441236bd.cwl | 120 +++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 138 +++++++++---------
4 files changed, 193 insertions(+), 73 deletions(-)
create mode 100644 .renku/workflow/d38156548319433aa76d8a44441236bd.cwl
diff --git a/.renku/workflow/d38156548319433aa76d8a44441236bd.cwl b/.renku/workflow/d38156548319433aa76d8a44441236bd.cwl
new file mode 100644
index 000000000..aac46e302
--- /dev/null
+++ b/.renku/workflow/d38156548319433aa76d8a44441236bd.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_0:
+ outputSource: step_1/output_1
+ streamable: false
+ type: Directory
+ output_2:
+ outputSource: step_1/output_0
+ streamable: false
+ type: File
+requirements: []
+steps:
+ step_1:
+ in:
+ input_1: input_1
+ input_2: input_2
+ input_3: input_3
+ input_4: input_4
+ out:
+ - output_0
+ - output_1
+ 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 9926028e4..3c2976451 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:da333aaf40c0db774f87c0654d56c45e72788eda6bb0ef0b253ecbb9e034b833
-size 21490192
+oid sha256:db2f6e5f2d8c29067e43dc70ea18465841f0a1851b624b085e4d8a891a81bf20
+size 21571126
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 81b7319b1..bfe4fe912 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:d97e049d903c4873e23cb051f9be8f2de29dae51670c0dc3002cb95b57e30dad
-size 147943
+oid sha256:d9833f5095ca0a847f00ab5622ab1be1ce68bcf61e3005431bb99627cdcd43ec
+size 149725
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 1cda5c38f..08cf9764e 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": 4.107006,
- "end_time": "2020-12-09T07:40:23.423926",
+ "duration": 6.57455,
+ "end_time": "2020-12-10T07:45:03.853676",
"exception": false,
- "start_time": "2020-12-09T07:40:19.316920",
+ "start_time": "2020-12-10T07:44:57.279126",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.023293,
- "end_time": "2020-12-09T07:40:23.461454",
+ "duration": 0.023212,
+ "end_time": "2020-12-10T07:45:03.894419",
"exception": false,
- "start_time": "2020-12-09T07:40:23.438161",
+ "start_time": "2020-12-10T07:45:03.871207",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.020651,
- "end_time": "2020-12-09T07:40:23.493997",
+ "duration": 0.026984,
+ "end_time": "2020-12-10T07:45:03.932218",
"exception": false,
- "start_time": "2020-12-09T07:40:23.473346",
+ "start_time": "2020-12-10T07:45:03.905234",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/benfs3jq/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/hjio672c/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": 0.007319,
- "end_time": "2020-12-09T07:40:23.508686",
+ "duration": 0.009132,
+ "end_time": "2020-12-10T07:45:03.952183",
"exception": false,
- "start_time": "2020-12-09T07:40:23.501367",
+ "start_time": "2020-12-10T07:45:03.943051",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.376143,
- "end_time": "2020-12-09T07:40:23.889965",
+ "duration": 0.838065,
+ "end_time": "2020-12-10T07:45:04.800589",
"exception": false,
- "start_time": "2020-12-09T07:40:23.513822",
+ "start_time": "2020-12-10T07:45:03.962524",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.023167,
- "end_time": "2020-12-09T07:40:23.927224",
+ "duration": 0.031905,
+ "end_time": "2020-12-10T07:45:04.847192",
"exception": false,
- "start_time": "2020-12-09T07:40:23.904057",
+ "start_time": "2020-12-10T07:45:04.815287",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.070755,
- "end_time": "2020-12-09T07:40:24.006782",
+ "duration": 0.114974,
+ "end_time": "2020-12-10T07:45:04.976342",
"exception": false,
- "start_time": "2020-12-09T07:40:23.936027",
+ "start_time": "2020-12-10T07:45:04.861368",
"status": "completed"
},
"tags": []
@@ -284,10 +284,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007971,
- "end_time": "2020-12-09T07:40:24.030072",
+ "duration": 0.011016,
+ "end_time": "2020-12-10T07:45:05.004437",
"exception": false,
- "start_time": "2020-12-09T07:40:24.022101",
+ "start_time": "2020-12-10T07:45:04.993421",
"status": "completed"
},
"tags": []
@@ -301,10 +301,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 35.628268,
- "end_time": "2020-12-09T07:40:59.665569",
+ "duration": 0.641805,
+ "end_time": "2020-12-10T07:45:05.655807",
"exception": false,
- "start_time": "2020-12-09T07:40:24.037301",
+ "start_time": "2020-12-10T07:45:05.014002",
"status": "completed"
},
"tags": []
@@ -321,10 +321,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.050121,
- "end_time": "2020-12-09T07:40:59.732700",
+ "duration": 0.055563,
+ "end_time": "2020-12-10T07:45:05.724800",
"exception": false,
- "start_time": "2020-12-09T07:40:59.682579",
+ "start_time": "2020-12-10T07:45:05.669237",
"status": "completed"
},
"tags": []
@@ -343,10 +343,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.623504,
- "end_time": "2020-12-09T07:41:00.368713",
+ "duration": 0.711583,
+ "end_time": "2020-12-10T07:45:06.452035",
"exception": false,
- "start_time": "2020-12-09T07:40:59.745209",
+ "start_time": "2020-12-10T07:45:05.740452",
"status": "completed"
},
"tags": []
@@ -356,7 +356,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "15745 data points\n"
+ "15801 data points\n"
]
},
{
@@ -406,21 +406,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201208</td>\n",
+ " <td>20201209</td>\n",
" <td>AK</td>\n",
- " <td>36758.0</td>\n",
+ " <td>37342.0</td>\n",
" <td>NaN</td>\n",
- " <td>1052220.0</td>\n",
+ " <td>1062213.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1088978.0</td>\n",
- " <td>159.0</td>\n",
- " <td>827.0</td>\n",
+ " <td>1099555.0</td>\n",
+ " <td>165.0</td>\n",
+ " <td>847.0</td>\n",
" <td>...</td>\n",
- " <td>1088978</td>\n",
- " <td>0</td>\n",
- " <td>22</td>\n",
- " <td>332692318da328d0239cf8586792c45a6c837366</td>\n",
+ " <td>1099555</td>\n",
+ " <td>4</td>\n",
+ " <td>20</td>\n",
+ " <td>1ff1db7b83dd9155a28a2e3687fbbb65d619643e</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>20201208</td>\n",
+ " <td>20201209</td>\n",
" <td>AL</td>\n",
- " <td>276665.0</td>\n",
- " <td>47658.0</td>\n",
- " <td>1435083.0</td>\n",
+ " <td>280187.0</td>\n",
+ " <td>48648.0</td>\n",
+ " <td>1441625.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsPeopleViral</td>\n",
- " <td>1664090.0</td>\n",
- " <td>2097.0</td>\n",
- " <td>27323.0</td>\n",
+ " <td>1673164.0</td>\n",
+ " <td>2111.0</td>\n",
+ " <td>27618.0</td>\n",
" <td>...</td>\n",
- " <td>1711748</td>\n",
- " <td>50</td>\n",
- " <td>279</td>\n",
- " <td>c863532e0b12a00cdb0a9e311c4d17f23651b03f</td>\n",
+ " <td>1721812</td>\n",
+ " <td>43</td>\n",
+ " <td>295</td>\n",
+ " <td>e16ff21c63db24182a3474993772040770f37424</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 20201208 AK 36758.0 NaN 1052220.0 NaN \n",
- "1 20201208 AL 276665.0 47658.0 1435083.0 NaN \n",
+ "0 20201209 AK 37342.0 NaN 1062213.0 NaN \n",
+ "1 20201209 AL 280187.0 48648.0 1441625.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 1088978.0 159.0 \n",
- "1 totalTestsPeopleViral 1664090.0 2097.0 \n",
+ "0 totalTestsViral 1099555.0 165.0 \n",
+ "1 totalTestsPeopleViral 1673164.0 2111.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 827.0 ... 1088978 0 22 \n",
- "1 27323.0 ... 1711748 50 279 \n",
+ "0 847.0 ... 1099555 4 20 \n",
+ "1 27618.0 ... 1721812 43 295 \n",
"\n",
" hash commercialScore \\\n",
- "0 332692318da328d0239cf8586792c45a6c837366 0 \n",
- "1 c863532e0b12a00cdb0a9e311c4d17f23651b03f 0 \n",
+ "0 1ff1db7b83dd9155a28a2e3687fbbb65d619643e 0 \n",
+ "1 e16ff21c63db24182a3474993772040770f37424 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": 42.81985,
- "end_time": "2020-12-09T07:41:00.692783",
+ "duration": 13.022997,
+ "end_time": "2020-12-10T07:45:06.880109",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/benfs3jq/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/hjio672c/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/benfs3jq/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/hjio672c/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-12-09T07:40:17.872933",
+ "start_time": "2020-12-10T07:44:53.857112",
"version": "1.1.0"
}
},
--
GitLab