From 06ef64ff3b272a554f8aa867a6cbb98aea66314e Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Mon, 13 Jul 2020 07:30:10 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../fa40d0c1c84b401196713f9c9a9b6df1.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/fa40d0c1c84b401196713f9c9a9b6df1.cwl
diff --git a/.renku/workflow/fa40d0c1c84b401196713f9c9a9b6df1.cwl b/.renku/workflow/fa40d0c1c84b401196713f9c9a9b6df1.cwl
new file mode 100644
index 000000000..8995f2c45
--- /dev/null
+++ b/.renku/workflow/fa40d0c1c84b401196713f9c9a9b6df1.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_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 6fd81809d..55def8128 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 sha256:73f61de66cd2a15ff2e0ceb296815adc2ccc34ba973b280ec56f866b5acce74a
-size 6660991
+oid sha256:51188c6706bb3e37906342960c7886cfe237c7e4386c6154a641bff53471203d
+size 6713509
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 003861938..cdc86b0d4 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:f6759b0ee0af9fedc9c0124f35b03ffd59cf4daaa247ac886a03e9c64fcf4f5a
-size 48564
+oid sha256:f2a56259b08d4681dc06622daf80beb5c233166cae41a97dcfbe6d87fe7068ce
+size 48663
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index d8f259e71..40ee45174 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": 1.253125,
- "end_time": "2020-07-12T07:30:09.585051",
+ "duration": 4.780722,
+ "end_time": "2020-07-13T07:30:09.120646",
"exception": false,
- "start_time": "2020-07-12T07:30:08.331926",
+ "start_time": "2020-07-13T07:30:04.339924",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.022579,
- "end_time": "2020-07-12T07:30:09.621097",
+ "duration": 0.018573,
+ "end_time": "2020-07-13T07:30:09.151957",
"exception": false,
- "start_time": "2020-07-12T07:30:09.598518",
+ "start_time": "2020-07-13T07:30:09.133384",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.021159,
- "end_time": "2020-07-12T07:30:09.650361",
+ "duration": 0.020336,
+ "end_time": "2020-07-13T07:30:09.180856",
"exception": false,
- "start_time": "2020-07-12T07:30:09.629202",
+ "start_time": "2020-07-13T07:30:09.160520",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/sy1d927i/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/to3ihk72/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": 0.006997,
- "end_time": "2020-07-12T07:30:09.664982",
+ "duration": 0.008035,
+ "end_time": "2020-07-13T07:30:09.198082",
"exception": false,
- "start_time": "2020-07-12T07:30:09.657985",
+ "start_time": "2020-07-13T07:30:09.190047",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 4.639997,
- "end_time": "2020-07-12T07:30:14.310806",
+ "duration": 0.099326,
+ "end_time": "2020-07-13T07:30:09.305690",
"exception": false,
- "start_time": "2020-07-12T07:30:09.670809",
+ "start_time": "2020-07-13T07:30:09.206364",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.030799,
- "end_time": "2020-07-12T07:30:14.355583",
+ "duration": 0.020007,
+ "end_time": "2020-07-13T07:30:09.337139",
"exception": false,
- "start_time": "2020-07-12T07:30:14.324784",
+ "start_time": "2020-07-13T07:30:09.317132",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.05518,
- "end_time": "2020-07-12T07:30:14.424858",
+ "duration": 0.068403,
+ "end_time": "2020-07-13T07:30:09.415513",
"exception": false,
- "start_time": "2020-07-12T07:30:14.369678",
+ "start_time": "2020-07-13T07:30:09.347110",
"status": "completed"
},
"tags": []
@@ -249,10 +249,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.00736,
- "end_time": "2020-07-12T07:30:14.443222",
+ "duration": 0.00806,
+ "end_time": "2020-07-13T07:30:09.432548",
"exception": false,
- "start_time": "2020-07-12T07:30:14.435862",
+ "start_time": "2020-07-13T07:30:09.424488",
"status": "completed"
},
"tags": []
@@ -266,10 +266,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.248125,
- "end_time": "2020-07-12T07:30:14.698024",
+ "duration": 0.304093,
+ "end_time": "2020-07-13T07:30:09.744820",
"exception": false,
- "start_time": "2020-07-12T07:30:14.449899",
+ "start_time": "2020-07-13T07:30:09.440727",
"status": "completed"
},
"tags": []
@@ -286,10 +286,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.038102,
- "end_time": "2020-07-12T07:30:14.752660",
+ "duration": 0.030586,
+ "end_time": "2020-07-13T07:30:09.788075",
"exception": false,
- "start_time": "2020-07-12T07:30:14.714558",
+ "start_time": "2020-07-13T07:30:09.757489",
"status": "completed"
},
"tags": []
@@ -308,10 +308,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.302876,
- "end_time": "2020-07-12T07:30:15.071285",
+ "duration": 0.324677,
+ "end_time": "2020-07-13T07:30:10.125728",
"exception": false,
- "start_time": "2020-07-12T07:30:14.768409",
+ "start_time": "2020-07-13T07:30:09.801051",
"status": "completed"
},
"tags": []
@@ -321,7 +321,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "7185 data points\n"
+ "7241 data points\n"
]
},
{
@@ -371,21 +371,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200711</td>\n",
+ " <td>20200712</td>\n",
" <td>AK</td>\n",
- " <td>1385.0</td>\n",
- " <td>141991.0</td>\n",
+ " <td>1479.0</td>\n",
+ " <td>143996.0</td>\n",
" <td>NaN</td>\n",
- " <td>31.0</td>\n",
+ " <td>27.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>1.0</td>\n",
+ " <td>0.0</td>\n",
" <td>...</td>\n",
- " <td>143376</td>\n",
+ " <td>145475</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
- " <td>d88f70b7bfa373ef0fb14998ccb0d0d3a9c806fb</td>\n",
+ " <td>a0d3d26cd6bfe23ff076e92f50acd2e1ee43cfc4</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>20200711</td>\n",
+ " <td>20200712</td>\n",
" <td>AL</td>\n",
- " <td>51947.0</td>\n",
- " <td>450073.0</td>\n",
+ " <td>53587.0</td>\n",
+ " <td>457919.0</td>\n",
" <td>NaN</td>\n",
" <td>1068.0</td>\n",
" <td>6745.0</td>\n",
" <td>NaN</td>\n",
- " <td>904.0</td>\n",
+ " <td>911.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>502020</td>\n",
- " <td>10</td>\n",
- " <td>3656</td>\n",
- " <td>d4bd3a01be0c8af28a542861a4de75cf38649a10</td>\n",
+ " <td>511506</td>\n",
+ " <td>7</td>\n",
+ " <td>0</td>\n",
+ " <td>fb4327f63eb6b270a2ead2bbdd438615bb7c361f</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 20200711 AK 1385.0 141991.0 NaN 31.0 \n",
- "1 20200711 AL 51947.0 450073.0 NaN 1068.0 \n",
+ "0 20200712 AK 1479.0 143996.0 NaN 27.0 \n",
+ "1 20200712 AL 53587.0 457919.0 NaN 1068.0 \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 6745.0 NaN 904.0 \n",
+ "1 6745.0 NaN 911.0 \n",
"\n",
" onVentilatorCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 1.0 ... 143376 0 0 \n",
- "1 NaN ... 502020 10 3656 \n",
+ "0 0.0 ... 145475 0 0 \n",
+ "1 NaN ... 511506 7 0 \n",
"\n",
" hash commercialScore \\\n",
- "0 d88f70b7bfa373ef0fb14998ccb0d0d3a9c806fb 0 \n",
- "1 d4bd3a01be0c8af28a542861a4de75cf38649a10 0 \n",
+ "0 a0d3d26cd6bfe23ff076e92f50acd2e1ee43cfc4 0 \n",
+ "1 fb4327f63eb6b270a2ead2bbdd438615bb7c361f 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": 8.131372,
- "end_time": "2020-07-12T07:30:15.397599",
+ "duration": 9.487183,
+ "end_time": "2020-07-13T07:30:10.445396",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/sy1d927i/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/to3ihk72/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/sy1d927i/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/to3ihk72/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-07-12T07:30:07.266227",
+ "start_time": "2020-07-13T07:30:00.958213",
"version": "1.1.0"
}
},
--
GitLab