diff --git a/.renku/workflow/e516f4782fbf46198f95f09a443ab7bc.cwl b/.renku/workflow/e516f4782fbf46198f95f09a443ab7bc.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..274898149f542535a07b77c86dec9ba172f193c3
--- /dev/null
+++ b/.renku/workflow/e516f4782fbf46198f95f09a443ab7bc.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_2:
+ 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 6dc685941d0b8dde6fd3e54611c3bc560aef39e8..67932f60d0bdfeaca80f10793401f50b9e377b7a 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 sha256:5c9f386beea81d36dc3af3c922a24ca01de76c669cd7d5c82ac7837de10899ca
-size 2386298
+oid sha256:24288640e85b223ff18176af4c03631e5ced4393e3e5c816774f0ffacc466580
+size 2421096
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 15ce8dfe2c1c16490ef9accb754010961de3c41b..3f1652976cdbfb6d310443a7e011f66fab724791 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:a1705de913d3e07ed73e7efa47c85dfece16620a73028c791305ec2ca086dc44
-size 30683
+oid sha256:7a3a85f6ac6d47f4924684d8d366d43341b5e81be1f09b83703fce9545e98eed
+size 32431
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index cb9f4f1f7cacc4598d301e695298c68f205c4741..5529737da2db02aafeba227781c43de3e4976573 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": 2.928467,
- "end_time": "2020-05-17T07:25:42.908503",
+ "duration": 0.593278,
+ "end_time": "2020-05-18T07:26:09.467232",
"exception": false,
- "start_time": "2020-05-17T07:25:39.980036",
+ "start_time": "2020-05-18T07:26:08.873954",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.021843,
- "end_time": "2020-05-17T07:25:42.941054",
+ "duration": 0.017725,
+ "end_time": "2020-05-18T07:26:09.497760",
"exception": false,
- "start_time": "2020-05-17T07:25:42.919211",
+ "start_time": "2020-05-18T07:26:09.480035",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.018345,
- "end_time": "2020-05-17T07:25:42.971315",
+ "duration": 0.021636,
+ "end_time": "2020-05-18T07:26:09.526773",
"exception": false,
- "start_time": "2020-05-17T07:25:42.952970",
+ "start_time": "2020-05-18T07:26:09.505137",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/9wpd3j7s/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/0cj0khu0/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": 0.008496,
- "end_time": "2020-05-17T07:25:42.988207",
+ "duration": 0.007174,
+ "end_time": "2020-05-18T07:26:09.544389",
"exception": false,
- "start_time": "2020-05-17T07:25:42.979711",
+ "start_time": "2020-05-18T07:26:09.537215",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 1.517465,
- "end_time": "2020-05-17T07:25:44.513111",
+ "duration": 1.054185,
+ "end_time": "2020-05-18T07:26:10.606531",
"exception": false,
- "start_time": "2020-05-17T07:25:42.995646",
+ "start_time": "2020-05-18T07:26:09.552346",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.024181,
- "end_time": "2020-05-17T07:25:44.555995",
+ "duration": 0.022713,
+ "end_time": "2020-05-18T07:26:10.643798",
"exception": false,
- "start_time": "2020-05-17T07:25:44.531814",
+ "start_time": "2020-05-18T07:26:10.621085",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.06814,
- "end_time": "2020-05-17T07:25:44.632953",
+ "duration": 0.064022,
+ "end_time": "2020-05-18T07:26:10.716677",
"exception": false,
- "start_time": "2020-05-17T07:25:44.564813",
+ "start_time": "2020-05-18T07:26:10.652655",
"status": "completed"
},
"tags": []
@@ -246,10 +246,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007891,
- "end_time": "2020-05-17T07:25:44.650482",
+ "duration": 0.008369,
+ "end_time": "2020-05-18T07:26:10.736609",
"exception": false,
- "start_time": "2020-05-17T07:25:44.642591",
+ "start_time": "2020-05-18T07:26:10.728240",
"status": "completed"
},
"tags": []
@@ -263,10 +263,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 4.727491,
- "end_time": "2020-05-17T07:25:49.386566",
+ "duration": 4.601402,
+ "end_time": "2020-05-18T07:26:15.346459",
"exception": false,
- "start_time": "2020-05-17T07:25:44.659075",
+ "start_time": "2020-05-18T07:26:10.745057",
"status": "completed"
},
"tags": []
@@ -283,10 +283,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.024029,
- "end_time": "2020-05-17T07:25:49.425475",
+ "duration": 0.027366,
+ "end_time": "2020-05-18T07:26:15.388220",
"exception": false,
- "start_time": "2020-05-17T07:25:49.401446",
+ "start_time": "2020-05-18T07:26:15.360854",
"status": "completed"
},
"tags": []
@@ -305,10 +305,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.150687,
- "end_time": "2020-05-17T07:25:49.586734",
+ "duration": 0.171187,
+ "end_time": "2020-05-18T07:26:15.569770",
"exception": false,
- "start_time": "2020-05-17T07:25:49.436047",
+ "start_time": "2020-05-18T07:26:15.398583",
"status": "completed"
},
"tags": []
@@ -318,7 +318,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "4049 data points\n"
+ "4105 data points\n"
]
},
{
@@ -368,51 +368,51 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200516</td>\n",
+ " <td>20200517</td>\n",
" <td>AK</td>\n",
- " <td>392.0</td>\n",
- " <td>32889.0</td>\n",
+ " <td>396.0</td>\n",
+ " <td>34255.0</td>\n",
" <td>NaN</td>\n",
- " <td>10.0</td>\n",
+ " <td>13.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
" <td>NaN</td>\n",
- " <td>33281</td>\n",
- " <td>33281</td>\n",
- " <td>33281</td>\n",
+ " <td>34651</td>\n",
+ " <td>34651</td>\n",
+ " <td>34651</td>\n",
" <td>2</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
- " <td>859.0</td>\n",
+ " <td>1366.0</td>\n",
" <td>4.0</td>\n",
- " <td>863.0</td>\n",
+ " <td>1370.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200516</td>\n",
+ " <td>20200517</td>\n",
" <td>AL</td>\n",
- " <td>11523.0</td>\n",
- " <td>141971.0</td>\n",
+ " <td>11771.0</td>\n",
+ " <td>144579.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>1387.0</td>\n",
+ " <td>1392.0</td>\n",
" <td>NaN</td>\n",
- " <td>501.0</td>\n",
+ " <td>504.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>1387.0</td>\n",
- " <td>153494</td>\n",
- " <td>153494</td>\n",
- " <td>153494</td>\n",
+ " <td>1392.0</td>\n",
+ " <td>156350</td>\n",
+ " <td>156350</td>\n",
+ " <td>156350</td>\n",
" <td>1</td>\n",
- " <td>9.0</td>\n",
- " <td>10.0</td>\n",
- " <td>7124.0</td>\n",
- " <td>307.0</td>\n",
- " <td>7431.0</td>\n",
+ " <td>3.0</td>\n",
+ " <td>5.0</td>\n",
+ " <td>2608.0</td>\n",
+ " <td>248.0</td>\n",
+ " <td>2856.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
@@ -421,24 +421,24 @@
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200516 AK 392.0 32889.0 NaN 10.0 \n",
- "1 20200516 AL 11523.0 141971.0 NaN NaN \n",
+ "0 20200517 AK 396.0 34255.0 NaN 13.0 \n",
+ "1 20200517 AL 11771.0 144579.0 NaN NaN \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 1387.0 NaN 501.0 \n",
+ "1 1392.0 NaN 504.0 \n",
"\n",
" onVentilatorCurrently ... hospitalized total totalTestResults posNeg \\\n",
- "0 NaN ... NaN 33281 33281 33281 \n",
- "1 NaN ... 1387.0 153494 153494 153494 \n",
+ "0 NaN ... NaN 34651 34651 34651 \n",
+ "1 NaN ... 1392.0 156350 156350 156350 \n",
"\n",
" fips deathIncrease hospitalizedIncrease negativeIncrease \\\n",
- "0 2 0.0 0.0 859.0 \n",
- "1 1 9.0 10.0 7124.0 \n",
+ "0 2 0.0 0.0 1366.0 \n",
+ "1 1 3.0 5.0 2608.0 \n",
"\n",
" positiveIncrease totalTestResultsIncrease \n",
- "0 4.0 863.0 \n",
- "1 307.0 7431.0 \n",
+ "0 4.0 1370.0 \n",
+ "1 248.0 2856.0 \n",
"\n",
"[2 rows x 27 columns]"
]
@@ -474,18 +474,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 11.296286,
- "end_time": "2020-05-17T07:25:49.910797",
+ "duration": 8.010656,
+ "end_time": "2020-05-18T07:26:15.893269",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/9wpd3j7s/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/0cj0khu0/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/9wpd3j7s/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/0cj0khu0/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-05-17T07:25:38.614511",
+ "start_time": "2020-05-18T07:26:07.882613",
"version": "1.1.0"
}
},