From 42af95f6ded2cbab43d3d6ad51e44351ea339954 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Mon, 2 Nov 2020 07:40:05 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../975694ae2995400c97fb3932cbfc6bc1.cwl | 120 +++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 124 +++++++++---------
4 files changed, 186 insertions(+), 66 deletions(-)
create mode 100644 .renku/workflow/975694ae2995400c97fb3932cbfc6bc1.cwl
diff --git a/.renku/workflow/975694ae2995400c97fb3932cbfc6bc1.cwl b/.renku/workflow/975694ae2995400c97fb3932cbfc6bc1.cwl
new file mode 100644
index 000000000..ee066a442
--- /dev/null
+++ b/.renku/workflow/975694ae2995400c97fb3932cbfc6bc1.cwl
@@ -0,0 +1,120 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: states-daily.json
+ streamable: false
+ type: string
+ input_2:
+ default: out_folder
+ streamable: false
+ type: string
+ input_3:
+ default: data/covidtracking
+ streamable: false
+ type: string
+ input_4:
+ default:
+ class: File
+ path: ../../notebooks/process/download-covidtracking-data.ipynb
+ streamable: false
+ type: File
+ input_5:
+ default: runs/download-covidtracking-data.runs.ipynb
+ streamable: false
+ type: string
+ input_6:
+ default: states-metadata.json
+ streamable: false
+ type: string
+outputs:
+ output_2:
+ outputSource: step_2/output_0
+ streamable: false
+ type: File
+ output_3:
+ outputSource: step_2/output_1
+ streamable: false
+ type: Directory
+requirements: []
+steps:
+ step_1:
+ in:
+ filename: input_1
+ input_directory: step_2/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_2:
+ in:
+ input_1: input_2
+ input_2: input_3
+ input_3: input_4
+ input_4: input_5
+ out:
+ - output_1
+ - output_0
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
+ step_3:
+ in:
+ filename: input_6
+ input_directory: step_2/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 a6c08f854..ed95224be 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 sha256:62d83a9e7e219b75a90a189b1afb7bc9b6bf64b0c1640f0a71d25ac2395c0017
-size 18536189
+oid sha256:136defefdadf4133e1d20028db3d077e4ea2d141eee730b645374fe90e0e94d7
+size 18613184
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index e377d225b..ab83d8c6d 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:e5c9982f4d81279d78cee5958a09ef5197dde0a9ac1d96cc2cb456bf4629da9d
-size 108379
+oid sha256:f4ec8171dd99613eb1b81ecffa35355fe64aa13a460cc8b1a0dd3949e8933a1d
+size 108213
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 014eaa71d..f8622d4e8 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": 5.037062,
- "end_time": "2020-11-01T07:37:45.933708",
+ "duration": 4.38731,
+ "end_time": "2020-11-02T07:40:01.538008",
"exception": false,
- "start_time": "2020-11-01T07:37:40.896646",
+ "start_time": "2020-11-02T07:39:57.150698",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.02828,
- "end_time": "2020-11-01T07:37:45.978315",
+ "duration": 0.024656,
+ "end_time": "2020-11-02T07:40:01.578884",
"exception": false,
- "start_time": "2020-11-01T07:37:45.950035",
+ "start_time": "2020-11-02T07:40:01.554228",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.022512,
- "end_time": "2020-11-01T07:37:46.013706",
+ "duration": 0.027968,
+ "end_time": "2020-11-02T07:40:01.620053",
"exception": false,
- "start_time": "2020-11-01T07:37:45.991194",
+ "start_time": "2020-11-02T07:40:01.592085",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/y_sxckx7/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/qj7q4luy/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": 0.006401,
- "end_time": "2020-11-01T07:37:46.029106",
+ "duration": 0.008125,
+ "end_time": "2020-11-02T07:40:01.638870",
"exception": false,
- "start_time": "2020-11-01T07:37:46.022705",
+ "start_time": "2020-11-02T07:40:01.630745",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.65798,
- "end_time": "2020-11-01T07:37:46.693110",
+ "duration": 1.010529,
+ "end_time": "2020-11-02T07:40:02.656587",
"exception": false,
- "start_time": "2020-11-01T07:37:46.035130",
+ "start_time": "2020-11-02T07:40:01.646058",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.028713,
- "end_time": "2020-11-01T07:37:46.735011",
+ "duration": 0.025484,
+ "end_time": "2020-11-02T07:40:02.696195",
"exception": false,
- "start_time": "2020-11-01T07:37:46.706298",
+ "start_time": "2020-11-02T07:40:02.670711",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.090248,
- "end_time": "2020-11-01T07:37:46.838574",
+ "duration": 0.081021,
+ "end_time": "2020-11-02T07:40:02.785478",
"exception": false,
- "start_time": "2020-11-01T07:37:46.748326",
+ "start_time": "2020-11-02T07:40:02.704457",
"status": "completed"
},
"tags": []
@@ -280,10 +280,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007958,
- "end_time": "2020-11-01T07:37:46.859707",
+ "duration": 0.008282,
+ "end_time": "2020-11-02T07:40:02.808385",
"exception": false,
- "start_time": "2020-11-01T07:37:46.851749",
+ "start_time": "2020-11-02T07:40:02.800103",
"status": "completed"
},
"tags": []
@@ -297,10 +297,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.437219,
- "end_time": "2020-11-01T07:37:47.303780",
+ "duration": 0.486308,
+ "end_time": "2020-11-02T07:40:03.301771",
"exception": false,
- "start_time": "2020-11-01T07:37:46.866561",
+ "start_time": "2020-11-02T07:40:02.815463",
"status": "completed"
},
"tags": []
@@ -317,10 +317,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.063124,
- "end_time": "2020-11-01T07:37:47.378855",
+ "duration": 0.06364,
+ "end_time": "2020-11-02T07:40:03.382133",
"exception": false,
- "start_time": "2020-11-01T07:37:47.315731",
+ "start_time": "2020-11-02T07:40:03.318493",
"status": "completed"
},
"tags": []
@@ -339,10 +339,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.650152,
- "end_time": "2020-11-01T07:37:48.043379",
+ "duration": 0.707388,
+ "end_time": "2020-11-02T07:40:04.104186",
"exception": false,
- "start_time": "2020-11-01T07:37:47.393227",
+ "start_time": "2020-11-02T07:40:03.396798",
"status": "completed"
},
"tags": []
@@ -352,7 +352,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "13607 data points\n"
+ "13663 data points\n"
]
},
{
@@ -402,21 +402,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201031</td>\n",
+ " <td>20201101</td>\n",
" <td>AK</td>\n",
- " <td>16355.0</td>\n",
+ " <td>16705.0</td>\n",
" <td>NaN</td>\n",
" <td>587852.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
" <td>604207.0</td>\n",
- " <td>94.0</td>\n",
+ " <td>98.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>604207</td>\n",
+ " <td>604557</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
- " <td>4fd1e9352fd403f75cd0f4b8c7d420de8eb73f0b</td>\n",
+ " <td>0fe81cb4b3a17588cfde8bbd309c3f0f2e786fd2</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>20201031</td>\n",
+ " <td>20201101</td>\n",
" <td>AL</td>\n",
- " <td>192285.0</td>\n",
- " <td>27990.0</td>\n",
- " <td>1181958.0</td>\n",
+ " <td>193985.0</td>\n",
+ " <td>28746.0</td>\n",
+ " <td>1187341.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1346253.0</td>\n",
- " <td>960.0</td>\n",
+ " <td>1352580.0</td>\n",
+ " <td>967.0</td>\n",
" <td>20450.0</td>\n",
" <td>...</td>\n",
- " <td>1374243</td>\n",
- " <td>35</td>\n",
+ " <td>1381326</td>\n",
+ " <td>6</td>\n",
" <td>0</td>\n",
- " <td>5194e1ea04ad4dace9ab68daca52f9fa98e39f1b</td>\n",
+ " <td>0bd0f2572848cf6f46a651c076d32afceb8dc6a1</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -455,20 +455,20 @@
],
"text/plain": [
" date state positive probableCases negative pending \\\n",
- "0 20201031 AK 16355.0 NaN 587852.0 NaN \n",
- "1 20201031 AL 192285.0 27990.0 1181958.0 NaN \n",
+ "0 20201101 AK 16705.0 NaN 587852.0 NaN \n",
+ "1 20201101 AL 193985.0 28746.0 1187341.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 604207.0 94.0 \n",
- "1 totalTestsViral 1346253.0 960.0 \n",
+ "0 totalTestsViral 604207.0 98.0 \n",
+ "1 totalTestsViral 1352580.0 967.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 NaN ... 604207 1 0 \n",
- "1 20450.0 ... 1374243 35 0 \n",
+ "0 NaN ... 604557 1 0 \n",
+ "1 20450.0 ... 1381326 6 0 \n",
"\n",
" hash commercialScore \\\n",
- "0 4fd1e9352fd403f75cd0f4b8c7d420de8eb73f0b 0 \n",
- "1 5194e1ea04ad4dace9ab68daca52f9fa98e39f1b 0 \n",
+ "0 0fe81cb4b3a17588cfde8bbd309c3f0f2e786fd2 0 \n",
+ "1 0bd0f2572848cf6f46a651c076d32afceb8dc6a1 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": 9.337475,
- "end_time": "2020-11-01T07:37:48.472569",
+ "duration": 9.174658,
+ "end_time": "2020-11-02T07:40:04.530883",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/y_sxckx7/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/qj7q4luy/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/y_sxckx7/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/qj7q4luy/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-11-01T07:37:39.135094",
+ "start_time": "2020-11-02T07:39:55.356225",
"version": "1.1.0"
}
},
--
GitLab