From 4d58c6eb9619b341ad4e12a054c43f3f75b18358 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Fri, 10 Jul 2020 07:30:45 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../c8b0e4f875e5472c82f15c37053cbbfd.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/c8b0e4f875e5472c82f15c37053cbbfd.cwl
diff --git a/.renku/workflow/c8b0e4f875e5472c82f15c37053cbbfd.cwl b/.renku/workflow/c8b0e4f875e5472c82f15c37053cbbfd.cwl
new file mode 100644
index 000000000..5e91f8298
--- /dev/null
+++ b/.renku/workflow/c8b0e4f875e5472c82f15c37053cbbfd.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_0:
+ outputSource: step_2/output_1
+ streamable: false
+ type: Directory
+ output_1:
+ outputSource: step_2/output_0
+ streamable: false
+ type: File
+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_0
+ - output_1
+ 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 6e0b71fd7..03926b5da 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 sha256:6d09adcf8e3867562152154cfb55e909478a0d08382f330dac1875b707a3d4ba
-size 6503444
+oid sha256:0f962505bcb6042a186eb3e383907fa325851842d829674dbefd29510a3f97fb
+size 6555942
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index f90ac7340..02c8b6753 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:ed5c9cc4193269f8be2970077387313776ee2405234a830b1e9d0373781e82d9
-size 48068
+oid sha256:5cc91a8c937cfb81a31702bb5fff19ebf56297295ea9b5eca63b414c6ba9fc72
+size 48163
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 19294340c..c208642f8 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": 4.359006,
- "end_time": "2020-07-09T07:30:08.774769",
+ "duration": 4.875701,
+ "end_time": "2020-07-10T07:30:43.715703",
"exception": false,
- "start_time": "2020-07-09T07:30:04.415763",
+ "start_time": "2020-07-10T07:30:38.840002",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.030327,
- "end_time": "2020-07-09T07:30:08.821783",
+ "duration": 0.017583,
+ "end_time": "2020-07-10T07:30:43.745704",
"exception": false,
- "start_time": "2020-07-09T07:30:08.791456",
+ "start_time": "2020-07-10T07:30:43.728121",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.023247,
- "end_time": "2020-07-09T07:30:08.858730",
+ "duration": 0.020528,
+ "end_time": "2020-07-10T07:30:43.773494",
"exception": false,
- "start_time": "2020-07-09T07:30:08.835483",
+ "start_time": "2020-07-10T07:30:43.752966",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/7998tnm6/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/zozi8wxi/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": 0.006754,
- "end_time": "2020-07-09T07:30:08.876050",
+ "duration": 0.007995,
+ "end_time": "2020-07-10T07:30:43.790951",
"exception": false,
- "start_time": "2020-07-09T07:30:08.869296",
+ "start_time": "2020-07-10T07:30:43.782956",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.185863,
- "end_time": "2020-07-09T07:30:09.068324",
+ "duration": 0.076221,
+ "end_time": "2020-07-10T07:30:43.874352",
"exception": false,
- "start_time": "2020-07-09T07:30:08.882461",
+ "start_time": "2020-07-10T07:30:43.798131",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.025901,
- "end_time": "2020-07-09T07:30:09.109237",
+ "duration": 0.021758,
+ "end_time": "2020-07-10T07:30:43.905004",
"exception": false,
- "start_time": "2020-07-09T07:30:09.083336",
+ "start_time": "2020-07-10T07:30:43.883246",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.078569,
- "end_time": "2020-07-09T07:30:09.197037",
+ "duration": 0.069709,
+ "end_time": "2020-07-10T07:30:43.983224",
"exception": false,
- "start_time": "2020-07-09T07:30:09.118468",
+ "start_time": "2020-07-10T07:30:43.913515",
"status": "completed"
},
"tags": []
@@ -249,10 +249,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007765,
- "end_time": "2020-07-09T07:30:09.217117",
+ "duration": 0.008943,
+ "end_time": "2020-07-10T07:30:44.001150",
"exception": false,
- "start_time": "2020-07-09T07:30:09.209352",
+ "start_time": "2020-07-10T07:30:43.992207",
"status": "completed"
},
"tags": []
@@ -266,10 +266,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.244587,
- "end_time": "2020-07-09T07:30:09.468401",
+ "duration": 0.227183,
+ "end_time": "2020-07-10T07:30:44.236566",
"exception": false,
- "start_time": "2020-07-09T07:30:09.223814",
+ "start_time": "2020-07-10T07:30:44.009383",
"status": "completed"
},
"tags": []
@@ -286,10 +286,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.027661,
- "end_time": "2020-07-09T07:30:09.515243",
+ "duration": 0.029433,
+ "end_time": "2020-07-10T07:30:44.278153",
"exception": false,
- "start_time": "2020-07-09T07:30:09.487582",
+ "start_time": "2020-07-10T07:30:44.248720",
"status": "completed"
},
"tags": []
@@ -308,10 +308,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.30228,
- "end_time": "2020-07-09T07:30:09.828236",
+ "duration": 0.311198,
+ "end_time": "2020-07-10T07:30:44.600669",
"exception": false,
- "start_time": "2020-07-09T07:30:09.525956",
+ "start_time": "2020-07-10T07:30:44.289471",
"status": "completed"
},
"tags": []
@@ -321,7 +321,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "7017 data points\n"
+ "7073 data points\n"
]
},
{
@@ -371,21 +371,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200708</td>\n",
+ " <td>20200709</td>\n",
" <td>AK</td>\n",
- " <td>1226.0</td>\n",
- " <td>132175.0</td>\n",
+ " <td>1272.0</td>\n",
+ " <td>134472.0</td>\n",
" <td>NaN</td>\n",
- " <td>30.0</td>\n",
+ " <td>28.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>0.0</td>\n",
" <td>...</td>\n",
- " <td>133401</td>\n",
+ " <td>135744</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
- " <td>44f40820165a4480d4a1b8b031bb7e6bf3a22a40</td>\n",
+ " <td>55912ff71f785e526d4154c6ddd12b7188f17807</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -395,21 +395,21 @@
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200708</td>\n",
+ " <td>20200709</td>\n",
" <td>AL</td>\n",
- " <td>46962.0</td>\n",
+ " <td>49174.0</td>\n",
" <td>421330.0</td>\n",
" <td>NaN</td>\n",
- " <td>1110.0</td>\n",
- " <td>3006.0</td>\n",
+ " <td>1125.0</td>\n",
+ " <td>3039.0</td>\n",
" <td>NaN</td>\n",
- " <td>871.0</td>\n",
+ " <td>877.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>468292</td>\n",
- " <td>25</td>\n",
- " <td>45</td>\n",
- " <td>9fc63c874a98fa97cfee6a65d2dff374513b499f</td>\n",
+ " <td>470504</td>\n",
+ " <td>10</td>\n",
+ " <td>33</td>\n",
+ " <td>ce6e123b52713c8777e9a0b9e97cc7253918fb4a</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -424,20 +424,20 @@
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200708 AK 1226.0 132175.0 NaN 30.0 \n",
- "1 20200708 AL 46962.0 421330.0 NaN 1110.0 \n",
+ "0 20200709 AK 1272.0 134472.0 NaN 28.0 \n",
+ "1 20200709 AL 49174.0 421330.0 NaN 1125.0 \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 3006.0 NaN 871.0 \n",
+ "1 3039.0 NaN 877.0 \n",
"\n",
" onVentilatorCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 0.0 ... 133401 0 0 \n",
- "1 NaN ... 468292 25 45 \n",
+ "0 0.0 ... 135744 0 0 \n",
+ "1 NaN ... 470504 10 33 \n",
"\n",
" hash commercialScore \\\n",
- "0 44f40820165a4480d4a1b8b031bb7e6bf3a22a40 0 \n",
- "1 9fc63c874a98fa97cfee6a65d2dff374513b499f 0 \n",
+ "0 55912ff71f785e526d4154c6ddd12b7188f17807 0 \n",
+ "1 ce6e123b52713c8777e9a0b9e97cc7253918fb4a 0 \n",
"\n",
" negativeRegularScore negativeScore positiveScore score grade \n",
"0 0 0 0 0 \n",
@@ -477,18 +477,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 8.238482,
- "end_time": "2020-07-09T07:30:10.254946",
+ "duration": 8.399002,
+ "end_time": "2020-07-10T07:30:44.935352",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/7998tnm6/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/zozi8wxi/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/7998tnm6/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/zozi8wxi/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-07-09T07:30:02.016464",
+ "start_time": "2020-07-10T07:30:36.536350",
"version": "1.1.0"
}
},
--
GitLab