From ac17e602f599e7fe55c746e01990d09fcdfcefb4 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Sat, 12 Dec 2020 07:38:08 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../3f85941e1428451fb4b69ba4d17a2f68.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/3f85941e1428451fb4b69ba4d17a2f68.cwl
diff --git a/.renku/workflow/3f85941e1428451fb4b69ba4d17a2f68.cwl b/.renku/workflow/3f85941e1428451fb4b69ba4d17a2f68.cwl
new file mode 100644
index 000000000..308b84ab3
--- /dev/null
+++ b/.renku/workflow/3f85941e1428451fb4b69ba4d17a2f68.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-metadata.json
+ streamable: false
+ type: string
+ input_6:
+ default: states-daily.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_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-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_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-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: []
diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index 3c2976451..b155be792 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:db2f6e5f2d8c29067e43dc70ea18465841f0a1851b624b085e4d8a891a81bf20
-size 21571126
+oid sha256:e62d080a170bc871e31539c8be8b3cdd3658cbe5d7fcf8a589eee3aefd0209e4
+size 21724952
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index bfe4fe912..4a863b13d 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:d9833f5095ca0a847f00ab5622ab1be1ce68bcf61e3005431bb99627cdcd43ec
-size 149725
+oid sha256:f2f507c8365cc03aedb8456a10e41bdea80f74fbd6ed14b16746c6968065691b
+size 150268
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 08cf9764e..ba4c0680b 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": 6.57455,
- "end_time": "2020-12-10T07:45:03.853676",
+ "duration": 6.889652,
+ "end_time": "2020-12-12T07:38:05.389643",
"exception": false,
- "start_time": "2020-12-10T07:44:57.279126",
+ "start_time": "2020-12-12T07:37:58.499991",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.023212,
- "end_time": "2020-12-10T07:45:03.894419",
+ "duration": 0.015644,
+ "end_time": "2020-12-12T07:38:05.417406",
"exception": false,
- "start_time": "2020-12-10T07:45:03.871207",
+ "start_time": "2020-12-12T07:38:05.401762",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.026984,
- "end_time": "2020-12-10T07:45:03.932218",
+ "duration": 0.010775,
+ "end_time": "2020-12-12T07:38:05.433035",
"exception": false,
- "start_time": "2020-12-10T07:45:03.905234",
+ "start_time": "2020-12-12T07:38:05.422260",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/hjio672c/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/r6lieysd/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": 0.009132,
- "end_time": "2020-12-10T07:45:03.952183",
+ "duration": 0.004017,
+ "end_time": "2020-12-12T07:38:05.441138",
"exception": false,
- "start_time": "2020-12-10T07:45:03.943051",
+ "start_time": "2020-12-12T07:38:05.437121",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.838065,
- "end_time": "2020-12-10T07:45:04.800589",
+ "duration": 0.343477,
+ "end_time": "2020-12-12T07:38:05.788838",
"exception": false,
- "start_time": "2020-12-10T07:45:03.962524",
+ "start_time": "2020-12-12T07:38:05.445361",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.031905,
- "end_time": "2020-12-10T07:45:04.847192",
+ "duration": 0.022185,
+ "end_time": "2020-12-12T07:38:05.822402",
"exception": false,
- "start_time": "2020-12-10T07:45:04.815287",
+ "start_time": "2020-12-12T07:38:05.800217",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.114974,
- "end_time": "2020-12-10T07:45:04.976342",
+ "duration": 0.071164,
+ "end_time": "2020-12-12T07:38:05.902998",
"exception": false,
- "start_time": "2020-12-10T07:45:04.861368",
+ "start_time": "2020-12-12T07:38:05.831834",
"status": "completed"
},
"tags": []
@@ -284,10 +284,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.011016,
- "end_time": "2020-12-10T07:45:05.004437",
+ "duration": 0.006768,
+ "end_time": "2020-12-12T07:38:05.921404",
"exception": false,
- "start_time": "2020-12-10T07:45:04.993421",
+ "start_time": "2020-12-12T07:38:05.914636",
"status": "completed"
},
"tags": []
@@ -301,10 +301,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.641805,
- "end_time": "2020-12-10T07:45:05.655807",
+ "duration": 0.644425,
+ "end_time": "2020-12-12T07:38:06.571920",
"exception": false,
- "start_time": "2020-12-10T07:45:05.014002",
+ "start_time": "2020-12-12T07:38:05.927495",
"status": "completed"
},
"tags": []
@@ -321,10 +321,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.055563,
- "end_time": "2020-12-10T07:45:05.724800",
+ "duration": 0.050735,
+ "end_time": "2020-12-12T07:38:06.639504",
"exception": false,
- "start_time": "2020-12-10T07:45:05.669237",
+ "start_time": "2020-12-12T07:38:06.588769",
"status": "completed"
},
"tags": []
@@ -343,10 +343,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.711583,
- "end_time": "2020-12-10T07:45:06.452035",
+ "duration": 0.614728,
+ "end_time": "2020-12-12T07:38:07.266668",
"exception": false,
- "start_time": "2020-12-10T07:45:05.740452",
+ "start_time": "2020-12-12T07:38:06.651940",
"status": "completed"
},
"tags": []
@@ -356,7 +356,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "15801 data points\n"
+ "15913 data points\n"
]
},
{
@@ -406,21 +406,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201209</td>\n",
+ " <td>20201211</td>\n",
" <td>AK</td>\n",
- " <td>37342.0</td>\n",
+ " <td>38584.0</td>\n",
" <td>NaN</td>\n",
- " <td>1062213.0</td>\n",
+ " <td>1084961.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1099555.0</td>\n",
- " <td>165.0</td>\n",
- " <td>847.0</td>\n",
+ " <td>1123545.0</td>\n",
+ " <td>146.0</td>\n",
+ " <td>869.0</td>\n",
" <td>...</td>\n",
- " <td>1099555</td>\n",
- " <td>4</td>\n",
- " <td>20</td>\n",
- " <td>1ff1db7b83dd9155a28a2e3687fbbb65d619643e</td>\n",
+ " <td>1123545</td>\n",
+ " <td>3</td>\n",
+ " <td>9</td>\n",
+ " <td>47f2cb8f9f01019549b85b0450c8c42c15bb3e77</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>20201209</td>\n",
+ " <td>20201211</td>\n",
" <td>AL</td>\n",
- " <td>280187.0</td>\n",
- " <td>48648.0</td>\n",
- " <td>1441625.0</td>\n",
+ " <td>288775.0</td>\n",
+ " <td>50896.0</td>\n",
+ " <td>1458560.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsPeopleViral</td>\n",
- " <td>1673164.0</td>\n",
+ " <td>1696439.0</td>\n",
" <td>2111.0</td>\n",
- " <td>27618.0</td>\n",
+ " <td>28146.0</td>\n",
" <td>...</td>\n",
- " <td>1721812</td>\n",
- " <td>43</td>\n",
- " <td>295</td>\n",
- " <td>e16ff21c63db24182a3474993772040770f37424</td>\n",
+ " <td>1747335</td>\n",
+ " <td>52</td>\n",
+ " <td>528</td>\n",
+ " <td>3bf1ccc167c9d139e7506942ea8f53c42bdeeab7</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 20201209 AK 37342.0 NaN 1062213.0 NaN \n",
- "1 20201209 AL 280187.0 48648.0 1441625.0 NaN \n",
+ "0 20201211 AK 38584.0 NaN 1084961.0 NaN \n",
+ "1 20201211 AL 288775.0 50896.0 1458560.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 1099555.0 165.0 \n",
- "1 totalTestsPeopleViral 1673164.0 2111.0 \n",
+ "0 totalTestsViral 1123545.0 146.0 \n",
+ "1 totalTestsPeopleViral 1696439.0 2111.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 847.0 ... 1099555 4 20 \n",
- "1 27618.0 ... 1721812 43 295 \n",
+ "0 869.0 ... 1123545 3 9 \n",
+ "1 28146.0 ... 1747335 52 528 \n",
"\n",
" hash commercialScore \\\n",
- "0 1ff1db7b83dd9155a28a2e3687fbbb65d619643e 0 \n",
- "1 e16ff21c63db24182a3474993772040770f37424 0 \n",
+ "0 47f2cb8f9f01019549b85b0450c8c42c15bb3e77 0 \n",
+ "1 3bf1ccc167c9d139e7506942ea8f53c42bdeeab7 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": 13.022997,
- "end_time": "2020-12-10T07:45:06.880109",
+ "duration": 10.7272,
+ "end_time": "2020-12-12T07:38:07.588984",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/hjio672c/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/r6lieysd/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/hjio672c/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/r6lieysd/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-12-10T07:44:53.857112",
+ "start_time": "2020-12-12T07:37:56.861784",
"version": "1.1.0"
}
},
--
GitLab