diff --git a/.renku/workflow/f54726462f944bd9a26bf8c0e84732d1.cwl b/.renku/workflow/f54726462f944bd9a26bf8c0e84732d1.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..bce7a62e91c51e09535a01b7efa4668be398c1cb
--- /dev/null
+++ b/.renku/workflow/f54726462f944bd9a26bf8c0e84732d1.cwl
@@ -0,0 +1,120 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: states-metadata.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-daily.json
+ streamable: false
+ type: string
+outputs:
+ output_2:
+ 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-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_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-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 26aad239989ffd6ace7f26709c9f35843d6c0e4d..60fc7bacc0dfae16417b07d76603cf8807df6488 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 sha256:4c0a2daee7f1f7dda568c39b8de42b496761e4686b1cc3429faeac0ee2261da3
-size 4205734
+oid sha256:f267857f071efbd257d39a8e53597a33766547cafe42a33c8fe223186c40a1af
+size 4803258
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 64f32c832c1ea69c9c0cea6efdf735bbb3d2875e..4cdbf31f50480a3b9c3322adbafeb81d4a75c742 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 sha256:15e431a1125ced9630804d815c544b1da67a5dffd8c8798393dc0c1db3014630
+oid sha256:b7f6ed28bdb6086871fec5a39085c151ec8b06e4e74304f4a6dac28966e241d1
size 37118
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 5b3dd4b09a7b1882b697fa61fbc830ef9d75684b..69e7931ba3cb6119cc9aefbb41909290ffe90c85 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": 1.522695,
- "end_time": "2020-06-10T11:15:28.287816",
+ "duration": 0.487122,
+ "end_time": "2020-06-11T07:27:32.572137",
"exception": false,
- "start_time": "2020-06-10T11:15:26.765121",
+ "start_time": "2020-06-11T07:27:32.085015",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.024235,
- "end_time": "2020-06-10T11:15:28.321893",
+ "duration": 0.021695,
+ "end_time": "2020-06-11T07:27:32.609291",
"exception": false,
- "start_time": "2020-06-10T11:15:28.297658",
+ "start_time": "2020-06-11T07:27:32.587596",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.024241,
- "end_time": "2020-06-10T11:15:28.355400",
+ "duration": 0.021591,
+ "end_time": "2020-06-11T07:27:32.641347",
"exception": false,
- "start_time": "2020-06-10T11:15:28.331159",
+ "start_time": "2020-06-11T07:27:32.619756",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/5m4uhyx2/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/iyyjg3ga/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": 0.008908,
- "end_time": "2020-06-10T11:15:28.373760",
+ "duration": 0.006855,
+ "end_time": "2020-06-11T07:27:32.657727",
"exception": false,
- "start_time": "2020-06-10T11:15:28.364852",
+ "start_time": "2020-06-11T07:27:32.650872",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.195406,
- "end_time": "2020-06-10T11:15:28.578569",
+ "duration": 0.171513,
+ "end_time": "2020-06-11T07:27:32.835574",
"exception": false,
- "start_time": "2020-06-10T11:15:28.383163",
+ "start_time": "2020-06-11T07:27:32.664061",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.02662,
- "end_time": "2020-06-10T11:15:28.614679",
+ "duration": 0.026162,
+ "end_time": "2020-06-11T07:27:32.876893",
"exception": false,
- "start_time": "2020-06-10T11:15:28.588059",
+ "start_time": "2020-06-11T07:27:32.850731",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.085122,
- "end_time": "2020-06-10T11:15:28.709239",
+ "duration": 0.074292,
+ "end_time": "2020-06-11T07:27:32.960997",
"exception": false,
- "start_time": "2020-06-10T11:15:28.624117",
+ "start_time": "2020-06-11T07:27:32.886705",
"status": "completed"
},
"tags": []
@@ -249,10 +249,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.009986,
- "end_time": "2020-06-10T11:15:28.730128",
+ "duration": 0.007967,
+ "end_time": "2020-06-11T07:27:32.983385",
"exception": false,
- "start_time": "2020-06-10T11:15:28.720142",
+ "start_time": "2020-06-11T07:27:32.975418",
"status": "completed"
},
"tags": []
@@ -266,10 +266,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.593309,
- "end_time": "2020-06-10T11:15:29.333873",
+ "duration": 0.191262,
+ "end_time": "2020-06-11T07:27:33.181607",
"exception": false,
- "start_time": "2020-06-10T11:15:28.740564",
+ "start_time": "2020-06-11T07:27:32.990345",
"status": "completed"
},
"tags": []
@@ -286,10 +286,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.029815,
- "end_time": "2020-06-10T11:15:29.382682",
+ "duration": 0.033195,
+ "end_time": "2020-06-11T07:27:33.231102",
"exception": false,
- "start_time": "2020-06-10T11:15:29.352867",
+ "start_time": "2020-06-11T07:27:33.197907",
"status": "completed"
},
"tags": []
@@ -308,10 +308,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.221971,
- "end_time": "2020-06-10T11:15:29.616007",
+ "duration": 0.210495,
+ "end_time": "2020-06-11T07:27:33.456670",
"exception": false,
- "start_time": "2020-06-10T11:15:29.394036",
+ "start_time": "2020-06-11T07:27:33.246175",
"status": "completed"
},
"tags": []
@@ -321,7 +321,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "5393 data points\n"
+ "5449 data points\n"
]
},
{
@@ -371,21 +371,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200609</td>\n",
+ " <td>20200610</td>\n",
" <td>AK</td>\n",
- " <td>573.0</td>\n",
- " <td>66317.0</td>\n",
+ " <td>593.0</td>\n",
+ " <td>67127.0</td>\n",
" <td>NaN</td>\n",
- " <td>12.0</td>\n",
+ " <td>22.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>1.0</td>\n",
+ " <td>3.0</td>\n",
" <td>...</td>\n",
- " <td>66890</td>\n",
- " <td>1</td>\n",
+ " <td>67720</td>\n",
+ " <td>0</td>\n",
" <td>0</td>\n",
- " <td>9eaf1802a047fc56612f95b6e8221d463088d951</td>\n",
+ " <td>c9486e6829e118950bb3df693089884e90df1761</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>20200609</td>\n",
+ " <td>20200610</td>\n",
" <td>AL</td>\n",
- " <td>21422.0</td>\n",
- " <td>246317.0</td>\n",
+ " <td>21989.0</td>\n",
+ " <td>251068.0</td>\n",
" <td>NaN</td>\n",
- " <td>600.0</td>\n",
- " <td>2087.0</td>\n",
+ " <td>629.0</td>\n",
+ " <td>2129.0</td>\n",
" <td>NaN</td>\n",
- " <td>631.0</td>\n",
+ " <td>646.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>267739</td>\n",
- " <td>11</td>\n",
- " <td>33</td>\n",
- " <td>efc4ed6259393a9d1a456d534f048bed440a3188</td>\n",
+ " <td>273057</td>\n",
+ " <td>15</td>\n",
+ " <td>42</td>\n",
+ " <td>19414d6567b3415847b4d4d5d4c191f2b954647f</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -419,31 +419,31 @@
" </tr>\n",
" </tbody>\n",
"</table>\n",
- "<p>2 rows × 35 columns</p>\n",
+ "<p>2 rows × 39 columns</p>\n",
"</div>"
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200609 AK 573.0 66317.0 NaN 12.0 \n",
- "1 20200609 AL 21422.0 246317.0 NaN 600.0 \n",
+ "0 20200610 AK 593.0 67127.0 NaN 22.0 \n",
+ "1 20200610 AL 21989.0 251068.0 NaN 629.0 \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 2087.0 NaN 631.0 \n",
+ "1 2129.0 NaN 646.0 \n",
"\n",
" onVentilatorCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 1.0 ... 66890 1 0 \n",
- "1 NaN ... 267739 11 33 \n",
+ "0 3.0 ... 67720 0 0 \n",
+ "1 NaN ... 273057 15 42 \n",
"\n",
" hash commercialScore \\\n",
- "0 9eaf1802a047fc56612f95b6e8221d463088d951 0 \n",
- "1 efc4ed6259393a9d1a456d534f048bed440a3188 0 \n",
+ "0 c9486e6829e118950bb3df693089884e90df1761 0 \n",
+ "1 19414d6567b3415847b4d4d5d4c191f2b954647f 0 \n",
"\n",
" negativeRegularScore negativeScore positiveScore score grade \n",
"0 0 0 0 0 \n",
"1 0 0 0 0 \n",
"\n",
- "[2 rows x 35 columns]"
+ "[2 rows x 39 columns]"
]
},
"execution_count": 9,
@@ -477,18 +477,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 4.292822,
- "end_time": "2020-06-10T11:15:29.939783",
+ "duration": 2.546059,
+ "end_time": "2020-06-11T07:27:33.780969",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/5m4uhyx2/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/iyyjg3ga/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/5m4uhyx2/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/iyyjg3ga/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-06-10T11:15:25.646961",
+ "start_time": "2020-06-11T07:27:31.234910",
"version": "1.1.0"
}
},