diff --git a/.renku/workflow/66f5307ec9194324b160ab1fd466e9d6.cwl b/.renku/workflow/66f5307ec9194324b160ab1fd466e9d6.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..8a0c1ca48375e3864462afa213879353525adfc9
--- /dev/null
+++ b/.renku/workflow/66f5307ec9194324b160ab1fd466e9d6.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-metadata.json
+ streamable: false
+ type: string
+ input_6:
+ default: states-daily.json
+ streamable: false
+ type: string
+outputs:
+ output_2:
+ 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-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
+ 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-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
+ - *id002
+ successCodes: []
+ temporaryFailCodes: []
diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index 8b8ad50a5fc04493153490e89c18c634d25aa820..1f039ac48b4730222085fae250ff4cc269f88438 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 sha256:20d05d8bf54fbe25d465293949d98baa8217af8455274ebf331eaa9fdecfc7b5
-size 3896218
+oid sha256:8cd217cca3afcedb310e36a7ea42508c92271044acc349992bea5abf79a05f6a
+size 3940450
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 82c95999ba447b51623e9410a48a12ff64ab2dd5..28ce6ebec8dbbdb3c80f0481e0268b8eb246533a 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 sha256:106cf31b2776e3d9c810972b8819576e6b9069017c01c9baf326178128121813
-size 34737
+oid sha256:8b0c5cfa8aedded7e57c76535faaa4f2b863b26d50909e984a39bbf6e8a5de59
+size 34797
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 7b7ab2ac3883501b755bfbe0f825062a7f5b3774..07cba5714688c37e81c12101d39897afdc54532e 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": 3.35233,
- "end_time": "2020-06-03T15:45:09.318776",
+ "duration": 4.627897,
+ "end_time": "2020-06-04T08:28:04.985732",
"exception": false,
- "start_time": "2020-06-03T15:45:05.966446",
+ "start_time": "2020-06-04T08:28:00.357835",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.0259,
- "end_time": "2020-06-03T15:45:09.361558",
+ "duration": 0.022291,
+ "end_time": "2020-06-04T08:28:05.020399",
"exception": false,
- "start_time": "2020-06-03T15:45:09.335658",
+ "start_time": "2020-06-04T08:28:04.998108",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.023503,
- "end_time": "2020-06-03T15:45:09.397029",
+ "duration": 0.022545,
+ "end_time": "2020-06-04T08:28:05.052282",
"exception": false,
- "start_time": "2020-06-03T15:45:09.373526",
+ "start_time": "2020-06-04T08:28:05.029737",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/eqrts4dp/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/m_83rm_4/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": 0.006779,
- "end_time": "2020-06-03T15:45:09.411335",
+ "duration": 0.007006,
+ "end_time": "2020-06-04T08:28:05.068409",
"exception": false,
- "start_time": "2020-06-03T15:45:09.404556",
+ "start_time": "2020-06-04T08:28:05.061403",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.597563,
- "end_time": "2020-06-03T15:45:10.014708",
+ "duration": 0.381514,
+ "end_time": "2020-06-04T08:28:05.457090",
"exception": false,
- "start_time": "2020-06-03T15:45:09.417145",
+ "start_time": "2020-06-04T08:28:05.075576",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.03125,
- "end_time": "2020-06-03T15:45:10.062585",
+ "duration": 0.027088,
+ "end_time": "2020-06-04T08:28:05.496958",
"exception": false,
- "start_time": "2020-06-03T15:45:10.031335",
+ "start_time": "2020-06-04T08:28:05.469870",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.091143,
- "end_time": "2020-06-03T15:45:10.164517",
+ "duration": 0.072587,
+ "end_time": "2020-06-04T08:28:05.580434",
"exception": false,
- "start_time": "2020-06-03T15:45:10.073374",
+ "start_time": "2020-06-04T08:28:05.507847",
"status": "completed"
},
"tags": []
@@ -242,10 +242,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008537,
- "end_time": "2020-06-03T15:45:10.188145",
+ "duration": 0.008248,
+ "end_time": "2020-06-04T08:28:05.598828",
"exception": false,
- "start_time": "2020-06-03T15:45:10.179608",
+ "start_time": "2020-06-04T08:28:05.590580",
"status": "completed"
},
"tags": []
@@ -259,10 +259,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 6.860154,
- "end_time": "2020-06-03T15:45:17.054999",
+ "duration": 0.154111,
+ "end_time": "2020-06-04T08:28:05.761833",
"exception": false,
- "start_time": "2020-06-03T15:45:10.194845",
+ "start_time": "2020-06-04T08:28:05.607722",
"status": "completed"
},
"tags": []
@@ -279,10 +279,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.036298,
- "end_time": "2020-06-03T15:45:17.109685",
+ "duration": 0.029699,
+ "end_time": "2020-06-04T08:28:05.803127",
"exception": false,
- "start_time": "2020-06-03T15:45:17.073387",
+ "start_time": "2020-06-04T08:28:05.773428",
"status": "completed"
},
"tags": []
@@ -301,10 +301,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.224468,
- "end_time": "2020-06-03T15:45:17.346605",
+ "duration": 0.20856,
+ "end_time": "2020-06-04T08:28:06.022260",
"exception": false,
- "start_time": "2020-06-03T15:45:17.122137",
+ "start_time": "2020-06-04T08:28:05.813700",
"status": "completed"
},
"tags": []
@@ -314,7 +314,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "5001 data points\n"
+ "5057 data points\n"
]
},
{
@@ -364,21 +364,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200602</td>\n",
+ " <td>20200603</td>\n",
" <td>AK</td>\n",
- " <td>487.0</td>\n",
- " <td>55716.0</td>\n",
+ " <td>505.0</td>\n",
+ " <td>57677.0</td>\n",
" <td>NaN</td>\n",
- " <td>10.0</td>\n",
+ " <td>11.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>0.0</td>\n",
" <td>...</td>\n",
- " <td>56203</td>\n",
+ " <td>58182</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
- " <td>8bfc576f3ce0c5438919ab2a672255d0630714ec</td>\n",
+ " <td>02548c93014e510ca02e0fc92122c299e4aa8e78</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -388,21 +388,21 @@
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200602</td>\n",
+ " <td>20200603</td>\n",
" <td>AL</td>\n",
- " <td>18642.0</td>\n",
- " <td>205160.0</td>\n",
+ " <td>18851.0</td>\n",
+ " <td>212743.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>1879.0</td>\n",
+ " <td>1900.0</td>\n",
" <td>NaN</td>\n",
" <td>591.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>223802</td>\n",
- " <td>5</td>\n",
- " <td>23</td>\n",
- " <td>e925d317dd6bba774728abaf5db247f3c5983394</td>\n",
+ " <td>231594</td>\n",
+ " <td>2</td>\n",
+ " <td>21</td>\n",
+ " <td>fe5df10e9c8639e15d2ce02d16d678e16f6f6cc7</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -417,20 +417,20 @@
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200602 AK 487.0 55716.0 NaN 10.0 \n",
- "1 20200602 AL 18642.0 205160.0 NaN NaN \n",
+ "0 20200603 AK 505.0 57677.0 NaN 11.0 \n",
+ "1 20200603 AL 18851.0 212743.0 NaN NaN \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 1879.0 NaN 591.0 \n",
+ "1 1900.0 NaN 591.0 \n",
"\n",
" onVentilatorCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 0.0 ... 56203 0 0 \n",
- "1 NaN ... 223802 5 23 \n",
+ "0 0.0 ... 58182 0 0 \n",
+ "1 NaN ... 231594 2 21 \n",
"\n",
" hash commercialScore \\\n",
- "0 8bfc576f3ce0c5438919ab2a672255d0630714ec 0 \n",
- "1 e925d317dd6bba774728abaf5db247f3c5983394 0 \n",
+ "0 02548c93014e510ca02e0fc92122c299e4aa8e78 0 \n",
+ "1 fe5df10e9c8639e15d2ce02d16d678e16f6f6cc7 0 \n",
"\n",
" negativeRegularScore negativeScore positiveScore score grade \n",
"0 0 0 0 0 \n",
@@ -470,18 +470,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 13.234479,
- "end_time": "2020-06-03T15:45:17.775676",
+ "duration": 7.919109,
+ "end_time": "2020-06-04T08:28:06.447225",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/eqrts4dp/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/m_83rm_4/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/eqrts4dp/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/m_83rm_4/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-06-03T15:45:04.541197",
+ "start_time": "2020-06-04T08:27:58.528116",
"version": "1.1.0"
}
},