diff --git a/.renku/workflow/6245936e8bb44ec5b660121c3735a626.cwl b/.renku/workflow/6245936e8bb44ec5b660121c3735a626.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..95851678e2d93cdf2268bd0df52b757fccb30963
--- /dev/null
+++ b/.renku/workflow/6245936e8bb44ec5b660121c3735a626.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_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 343c8082abb1b6f528857b792579426064b99075..6233cbf3a78a4505d6b847484014f515fdcd2f38 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 sha256:2343ced246db10e9804dceea377803c44955a9910d908be34e31999eb49d44ad
-size 18175761
+oid sha256:e6086cb19690e6a1a340496a347395b5659b0d571e797e56fe75f22382cfe0de
+size 18253505
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 29a4bc5e17a625b813e59444d1f4f61836fb0909..531ba2ba232bcb533d06058af5477d1d5d9f08a1 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:a866180dc4ac2f049894dfba83da40d06ce9d379c946e3f2f9290a0f95049aaf
-size 103619
+oid sha256:2a42c427de85fd5f0b2dca4993f4ec06a324f092e0b703bcded87c50defc65b7
+size 104080
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index aacfac40418f7dcb5192ce3f15d5789f5c9dd054..38226a095b7648d1ba32e851fa06d24c436d1617 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": 4.388415,
- "end_time": "2020-10-28T07:38:34.502247",
+ "duration": 4.537249,
+ "end_time": "2020-10-29T07:39:06.222092",
"exception": false,
- "start_time": "2020-10-28T07:38:30.113832",
+ "start_time": "2020-10-29T07:39:01.684843",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.023367,
- "end_time": "2020-10-28T07:38:34.542142",
+ "duration": 0.021881,
+ "end_time": "2020-10-29T07:39:06.258241",
"exception": false,
- "start_time": "2020-10-28T07:38:34.518775",
+ "start_time": "2020-10-29T07:39:06.236360",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.020044,
- "end_time": "2020-10-28T07:38:34.570219",
+ "duration": 0.027575,
+ "end_time": "2020-10-29T07:39:06.297922",
"exception": false,
- "start_time": "2020-10-28T07:38:34.550175",
+ "start_time": "2020-10-29T07:39:06.270347",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/_0d2bb1o/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/42lwuooh/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": 0.005427,
- "end_time": "2020-10-28T07:38:34.582403",
+ "duration": 0.007823,
+ "end_time": "2020-10-29T07:39:06.317748",
"exception": false,
- "start_time": "2020-10-28T07:38:34.576976",
+ "start_time": "2020-10-29T07:39:06.309925",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.869465,
- "end_time": "2020-10-28T07:38:35.457664",
+ "duration": 0.384563,
+ "end_time": "2020-10-29T07:39:06.710425",
"exception": false,
- "start_time": "2020-10-28T07:38:34.588199",
+ "start_time": "2020-10-29T07:39:06.325862",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.023801,
- "end_time": "2020-10-28T07:38:35.494930",
+ "duration": 0.023132,
+ "end_time": "2020-10-29T07:39:06.744099",
"exception": false,
- "start_time": "2020-10-28T07:38:35.471129",
+ "start_time": "2020-10-29T07:39:06.720967",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.085511,
- "end_time": "2020-10-28T07:38:35.588944",
+ "duration": 0.110546,
+ "end_time": "2020-10-29T07:39:06.864298",
"exception": false,
- "start_time": "2020-10-28T07:38:35.503433",
+ "start_time": "2020-10-29T07:39:06.753752",
"status": "completed"
},
"tags": []
@@ -280,10 +280,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007957,
- "end_time": "2020-10-28T07:38:35.610958",
+ "duration": 0.009476,
+ "end_time": "2020-10-29T07:39:06.883639",
"exception": false,
- "start_time": "2020-10-28T07:38:35.603001",
+ "start_time": "2020-10-29T07:39:06.874163",
"status": "completed"
},
"tags": []
@@ -297,10 +297,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.711259,
- "end_time": "2020-10-28T07:38:36.329223",
+ "duration": 30.429905,
+ "end_time": "2020-10-29T07:39:37.322953",
"exception": false,
- "start_time": "2020-10-28T07:38:35.617964",
+ "start_time": "2020-10-29T07:39:06.893048",
"status": "completed"
},
"tags": []
@@ -317,10 +317,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.060408,
- "end_time": "2020-10-28T07:38:36.405873",
+ "duration": 0.053599,
+ "end_time": "2020-10-29T07:39:37.390618",
"exception": false,
- "start_time": "2020-10-28T07:38:36.345465",
+ "start_time": "2020-10-29T07:39:37.337019",
"status": "completed"
},
"tags": []
@@ -339,10 +339,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.605678,
- "end_time": "2020-10-28T07:38:37.024275",
+ "duration": 0.701681,
+ "end_time": "2020-10-29T07:39:38.103517",
"exception": false,
- "start_time": "2020-10-28T07:38:36.418597",
+ "start_time": "2020-10-29T07:39:37.401836",
"status": "completed"
},
"tags": []
@@ -352,7 +352,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "13360 data points\n"
+ "13416 data points\n"
]
},
{
@@ -402,21 +402,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201027</td>\n",
+ " <td>20201028</td>\n",
" <td>AK</td>\n",
- " <td>14798.0</td>\n",
+ " <td>15155.0</td>\n",
" <td>NaN</td>\n",
- " <td>562631.0</td>\n",
+ " <td>565444.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>577429.0</td>\n",
- " <td>81.0</td>\n",
+ " <td>580599.0</td>\n",
+ " <td>80.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>577429</td>\n",
- " <td>2</td>\n",
+ " <td>580599</td>\n",
+ " <td>1</td>\n",
" <td>0</td>\n",
- " <td>7e2c10c46a59bf7b86096ce9df6bc962cab5cb74</td>\n",
+ " <td>f0f48cae1ff48cce0b1dfa2a67c30709261bf7f5</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>20201027</td>\n",
+ " <td>20201028</td>\n",
" <td>AL</td>\n",
- " <td>186437.0</td>\n",
- " <td>26998.0</td>\n",
- " <td>1153448.0</td>\n",
+ " <td>187706.0</td>\n",
+ " <td>27326.0</td>\n",
+ " <td>1159926.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1312887.0</td>\n",
- " <td>1001.0</td>\n",
- " <td>19974.0</td>\n",
+ " <td>1320306.0</td>\n",
+ " <td>1013.0</td>\n",
+ " <td>20116.0</td>\n",
" <td>...</td>\n",
- " <td>1339885</td>\n",
- " <td>26</td>\n",
- " <td>0</td>\n",
- " <td>fcc11dfcba1953aae8cbf7a4a63b867f3a4ec519</td>\n",
+ " <td>1347632</td>\n",
+ " <td>19</td>\n",
+ " <td>142</td>\n",
+ " <td>c713ea2c14a2c1435e7c7cbada7a09af31a376a6</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 20201027 AK 14798.0 NaN 562631.0 NaN \n",
- "1 20201027 AL 186437.0 26998.0 1153448.0 NaN \n",
+ "0 20201028 AK 15155.0 NaN 565444.0 NaN \n",
+ "1 20201028 AL 187706.0 27326.0 1159926.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 577429.0 81.0 \n",
- "1 totalTestsViral 1312887.0 1001.0 \n",
+ "0 totalTestsViral 580599.0 80.0 \n",
+ "1 totalTestsViral 1320306.0 1013.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 NaN ... 577429 2 0 \n",
- "1 19974.0 ... 1339885 26 0 \n",
+ "0 NaN ... 580599 1 0 \n",
+ "1 20116.0 ... 1347632 19 142 \n",
"\n",
" hash commercialScore \\\n",
- "0 7e2c10c46a59bf7b86096ce9df6bc962cab5cb74 0 \n",
- "1 fcc11dfcba1953aae8cbf7a4a63b867f3a4ec519 0 \n",
+ "0 f0f48cae1ff48cce0b1dfa2a67c30709261bf7f5 0 \n",
+ "1 c713ea2c14a2c1435e7c7cbada7a09af31a376a6 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": 8.602446,
- "end_time": "2020-10-28T07:38:37.450702",
+ "duration": 39.630647,
+ "end_time": "2020-10-29T07:39:38.423262",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/_0d2bb1o/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/42lwuooh/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/_0d2bb1o/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/42lwuooh/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-10-28T07:38:28.848256",
+ "start_time": "2020-10-29T07:38:58.792615",
"version": "1.1.0"
}
},