diff --git a/.renku/workflow/0c0a1f3296e7449eabc111d554d13407.cwl b/.renku/workflow/0c0a1f3296e7449eabc111d554d13407.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..a61366fbb14cf6c0c93e8265a615371ebba16a4e
--- /dev/null
+++ b/.renku/workflow/0c0a1f3296e7449eabc111d554d13407.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_0:
+ outputSource: step_1/output_1
+ streamable: false
+ type: Directory
+ output_3:
+ outputSource: step_1/output_0
+ streamable: false
+ type: File
+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 e1492264b31710679ca452ae8fb017795263c7de..60282837238789c6bb595b9207843a2bf5a493dd 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:a7eb7aef4ee7265a297111f782ed00b8d526db3edee85119645a3beea58460ae
-size 4117317
+oid sha256:0410311546426a662704b13dcd94d577d9078eecae82250d6a6ef6d778421309
+size 4161502
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 92f401e01b49de84efe724beef8a0dde5aadcde8..64f32c832c1ea69c9c0cea6efdf735bbb3d2875e 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 sha256:9033571a9181448e7ff67a380af843acbc76facc53b4939098b549d308cd2cd8
-size 37077
+oid sha256:15e431a1125ced9630804d815c544b1da67a5dffd8c8798393dc0c1db3014630
+size 37118
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 8b86ceae12b80dc4c9161073e529bd54f04438d3..39ac99f3ce3241c17ef5c30ad41de3678920c5a5 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": 2.264356,
- "end_time": "2020-06-08T07:27:00.606454",
+ "duration": 3.351525,
+ "end_time": "2020-06-09T07:28:13.679272",
"exception": false,
- "start_time": "2020-06-08T07:26:58.342098",
+ "start_time": "2020-06-09T07:28:10.327747",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.018107,
- "end_time": "2020-06-08T07:27:00.634246",
+ "duration": 0.028314,
+ "end_time": "2020-06-09T07:28:13.724400",
"exception": false,
- "start_time": "2020-06-08T07:27:00.616139",
+ "start_time": "2020-06-09T07:28:13.696086",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.019065,
- "end_time": "2020-06-08T07:27:00.660974",
+ "duration": 0.024488,
+ "end_time": "2020-06-09T07:28:13.763732",
"exception": false,
- "start_time": "2020-06-08T07:27:00.641909",
+ "start_time": "2020-06-09T07:28:13.739244",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/88sodlj1/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/mfmoq2hy/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": 0.008413,
- "end_time": "2020-06-08T07:27:00.678512",
+ "duration": 0.00777,
+ "end_time": "2020-06-09T07:28:13.786176",
"exception": false,
- "start_time": "2020-06-08T07:27:00.670099",
+ "start_time": "2020-06-09T07:28:13.778406",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.173251,
- "end_time": "2020-06-08T07:27:00.859073",
+ "duration": 0.201725,
+ "end_time": "2020-06-09T07:28:13.993473",
"exception": false,
- "start_time": "2020-06-08T07:27:00.685822",
+ "start_time": "2020-06-09T07:28:13.791748",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.022117,
- "end_time": "2020-06-08T07:27:00.892647",
+ "duration": 0.027435,
+ "end_time": "2020-06-09T07:28:14.035753",
"exception": false,
- "start_time": "2020-06-08T07:27:00.870530",
+ "start_time": "2020-06-09T07:28:14.008318",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.068642,
- "end_time": "2020-06-08T07:27:00.970730",
+ "duration": 0.072843,
+ "end_time": "2020-06-09T07:28:14.120811",
"exception": false,
- "start_time": "2020-06-08T07:27:00.902088",
+ "start_time": "2020-06-09T07:28:14.047968",
"status": "completed"
},
"tags": []
@@ -249,10 +249,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008121,
- "end_time": "2020-06-08T07:27:00.990910",
+ "duration": 0.008497,
+ "end_time": "2020-06-09T07:28:14.143970",
"exception": false,
- "start_time": "2020-06-08T07:27:00.982789",
+ "start_time": "2020-06-09T07:28:14.135473",
"status": "completed"
},
"tags": []
@@ -266,10 +266,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.640874,
- "end_time": "2020-06-08T07:27:01.639961",
+ "duration": 0.388675,
+ "end_time": "2020-06-09T07:28:14.539727",
"exception": false,
- "start_time": "2020-06-08T07:27:00.999087",
+ "start_time": "2020-06-09T07:28:14.151052",
"status": "completed"
},
"tags": []
@@ -286,10 +286,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.024747,
- "end_time": "2020-06-08T07:27:01.676632",
+ "duration": 0.032497,
+ "end_time": "2020-06-09T07:28:14.590724",
"exception": false,
- "start_time": "2020-06-08T07:27:01.651885",
+ "start_time": "2020-06-09T07:28:14.558227",
"status": "completed"
},
"tags": []
@@ -308,10 +308,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.207692,
- "end_time": "2020-06-08T07:27:01.895423",
+ "duration": 0.199498,
+ "end_time": "2020-06-09T07:28:14.803254",
"exception": false,
- "start_time": "2020-06-08T07:27:01.687731",
+ "start_time": "2020-06-09T07:28:14.603756",
"status": "completed"
},
"tags": []
@@ -321,7 +321,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "5281 data points\n"
+ "5337 data points\n"
]
},
{
@@ -371,21 +371,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200607</td>\n",
+ " <td>20200608</td>\n",
" <td>AK</td>\n",
- " <td>544.0</td>\n",
- " <td>64360.0</td>\n",
+ " <td>563.0</td>\n",
+ " <td>65349.0</td>\n",
" <td>NaN</td>\n",
" <td>7.0</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>64904</td>\n",
+ " <td>65912</td>\n",
" <td>0</td>\n",
- " <td>-48</td>\n",
- " <td>62adbd451838656b7df7519e830d6439be0b5877</td>\n",
+ " <td>0</td>\n",
+ " <td>06594e7f361ff9a5128a34de7a6f674b27c067ed</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>20200607</td>\n",
+ " <td>20200608</td>\n",
" <td>AL</td>\n",
- " <td>20500.0</td>\n",
+ " <td>20925.0</td>\n",
" <td>239066.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>2022.0</td>\n",
+ " <td>2054.0</td>\n",
" <td>NaN</td>\n",
- " <td>615.0</td>\n",
+ " <td>623.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>259566</td>\n",
- " <td>3</td>\n",
- " <td>29</td>\n",
- " <td>9040674078ce6afca363f8e95943845a032ab5d6</td>\n",
+ " <td>259991</td>\n",
+ " <td>26</td>\n",
+ " <td>32</td>\n",
+ " <td>b8596160c71e9a7a19933497105b33a6f96ab6f4</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 20200607 AK 544.0 64360.0 NaN 7.0 \n",
- "1 20200607 AL 20500.0 239066.0 NaN NaN \n",
+ "0 20200608 AK 563.0 65349.0 NaN 7.0 \n",
+ "1 20200608 AL 20925.0 239066.0 NaN NaN \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 2022.0 NaN 615.0 \n",
+ "1 2054.0 NaN 623.0 \n",
"\n",
" onVentilatorCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 1.0 ... 64904 0 -48 \n",
- "1 NaN ... 259566 3 29 \n",
+ "0 0.0 ... 65912 0 0 \n",
+ "1 NaN ... 259991 26 32 \n",
"\n",
" hash commercialScore \\\n",
- "0 62adbd451838656b7df7519e830d6439be0b5877 0 \n",
- "1 9040674078ce6afca363f8e95943845a032ab5d6 0 \n",
+ "0 06594e7f361ff9a5128a34de7a6f674b27c067ed 0 \n",
+ "1 b8596160c71e9a7a19933497105b33a6f96ab6f4 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": 6.083115,
- "end_time": "2020-06-08T07:27:02.218207",
+ "duration": 6.369763,
+ "end_time": "2020-06-09T07:28:15.128265",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/88sodlj1/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/mfmoq2hy/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/88sodlj1/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/mfmoq2hy/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-06-08T07:26:56.135092",
+ "start_time": "2020-06-09T07:28:08.758502",
"version": "1.1.0"
}
},