diff --git a/.renku/workflow/20c86d3d7885417b805f91afd932a627.cwl b/.renku/workflow/20c86d3d7885417b805f91afd932a627.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..a8e35b68b1209ea481386bf236383679302cee0b
--- /dev/null
+++ b/.renku/workflow/20c86d3d7885417b805f91afd932a627.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_1:
+ 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 1be11444642e4f974ac224f70975e82fec993ad0..ce3fa2695f12f9b0422fac3d113a07d005108b7c 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 sha256:8c1ab862b0edc7d2ec86cb1515e0ef920fa2ce0c5fd5b4a7fd928e9c54c8868e
-size 8291546
+oid sha256:5acd8695ad7773e3784bbabfb54e3e6a3379c968894f5c37e545b88d92bd676b
+size 8344111
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 1394cf3fd636295c7c3611c72b850bed9ac7cb61..9c523018f35660e2eb6afa8ae6fc8726a55ce041 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 sha256:5eb6e8452ea20eac3ffa209e980ad6bc8feedcc70773855978038d614336ef2a
-size 59497
+oid sha256:4ce25de8d46e9a0c7f96e7ab57cbc6fcf3a943ff2fd37a183678b83f428f36ec
+size 60597
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 3a6a7edd3d2602bf2bd8350b7a6a429d14635676..b9510f70402cb5c1738a99a8f3775328e6623b47 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": 4.909303,
- "end_time": "2020-08-12T07:32:52.940667",
+ "duration": 2.138843,
+ "end_time": "2020-08-13T07:32:08.076759",
"exception": false,
- "start_time": "2020-08-12T07:32:48.031364",
+ "start_time": "2020-08-13T07:32:05.937916",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.020786,
- "end_time": "2020-08-12T07:32:52.974199",
+ "duration": 0.019514,
+ "end_time": "2020-08-13T07:32:08.109425",
"exception": false,
- "start_time": "2020-08-12T07:32:52.953413",
+ "start_time": "2020-08-13T07:32:08.089911",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.018808,
- "end_time": "2020-08-12T07:32:53.002848",
+ "duration": 0.020546,
+ "end_time": "2020-08-13T07:32:08.138868",
"exception": false,
- "start_time": "2020-08-12T07:32:52.984040",
+ "start_time": "2020-08-13T07:32:08.118322",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/fa34vlpr/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/8ktvuu43/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": 0.007114,
- "end_time": "2020-08-12T07:32:53.017421",
+ "duration": 0.007322,
+ "end_time": "2020-08-13T07:32:08.155663",
"exception": false,
- "start_time": "2020-08-12T07:32:53.010307",
+ "start_time": "2020-08-13T07:32:08.148341",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.253919,
- "end_time": "2020-08-12T07:32:53.278771",
+ "duration": 0.288666,
+ "end_time": "2020-08-13T07:32:08.451980",
"exception": false,
- "start_time": "2020-08-12T07:32:53.024852",
+ "start_time": "2020-08-13T07:32:08.163314",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.023702,
- "end_time": "2020-08-12T07:32:53.315338",
+ "duration": 0.021771,
+ "end_time": "2020-08-13T07:32:08.485568",
"exception": false,
- "start_time": "2020-08-12T07:32:53.291636",
+ "start_time": "2020-08-13T07:32:08.463797",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.112023,
- "end_time": "2020-08-12T07:32:53.437535",
+ "duration": 0.075526,
+ "end_time": "2020-08-13T07:32:08.570959",
"exception": false,
- "start_time": "2020-08-12T07:32:53.325512",
+ "start_time": "2020-08-13T07:32:08.495433",
"status": "completed"
},
"tags": []
@@ -249,10 +249,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.010012,
- "end_time": "2020-08-12T07:32:53.458945",
+ "duration": 0.008029,
+ "end_time": "2020-08-13T07:32:08.591772",
"exception": false,
- "start_time": "2020-08-12T07:32:53.448933",
+ "start_time": "2020-08-13T07:32:08.583743",
"status": "completed"
},
"tags": []
@@ -266,10 +266,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.847674,
- "end_time": "2020-08-12T07:32:54.316583",
+ "duration": 0.912442,
+ "end_time": "2020-08-13T07:32:09.512304",
"exception": false,
- "start_time": "2020-08-12T07:32:53.468909",
+ "start_time": "2020-08-13T07:32:08.599862",
"status": "completed"
},
"tags": []
@@ -286,10 +286,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.034853,
- "end_time": "2020-08-12T07:32:54.363904",
+ "duration": 0.032626,
+ "end_time": "2020-08-13T07:32:09.560190",
"exception": false,
- "start_time": "2020-08-12T07:32:54.329051",
+ "start_time": "2020-08-13T07:32:09.527564",
"status": "completed"
},
"tags": []
@@ -308,10 +308,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.359212,
- "end_time": "2020-08-12T07:32:54.737206",
+ "duration": 0.363787,
+ "end_time": "2020-08-13T07:32:09.935148",
"exception": false,
- "start_time": "2020-08-12T07:32:54.377994",
+ "start_time": "2020-08-13T07:32:09.571361",
"status": "completed"
},
"tags": []
@@ -321,7 +321,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "8921 data points\n"
+ "8977 data points\n"
]
},
{
@@ -371,21 +371,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200811</td>\n",
+ " <td>20200812</td>\n",
" <td>AK</td>\n",
- " <td>4589.0</td>\n",
- " <td>286155.0</td>\n",
+ " <td>4655.0</td>\n",
+ " <td>287927.0</td>\n",
" <td>NaN</td>\n",
" <td>39.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>4.0</td>\n",
+ " <td>3.0</td>\n",
" <td>...</td>\n",
- " <td>290744</td>\n",
- " <td>0</td>\n",
+ " <td>292582</td>\n",
+ " <td>1</td>\n",
" <td>0</td>\n",
- " <td>75189f7e45df3d19bc61fc8790a6df68e33c41e4</td>\n",
+ " <td>04d3f681722d466f15660e1ded53888693484520</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>20200811</td>\n",
+ " <td>20200812</td>\n",
" <td>AL</td>\n",
- " <td>103851.0</td>\n",
- " <td>679838.0</td>\n",
+ " <td>104786.0</td>\n",
+ " <td>690985.0</td>\n",
" <td>NaN</td>\n",
- " <td>1506.0</td>\n",
- " <td>12070.0</td>\n",
+ " <td>1372.0</td>\n",
+ " <td>12292.0</td>\n",
" <td>NaN</td>\n",
- " <td>1270.0</td>\n",
+ " <td>1282.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>783689</td>\n",
- " <td>50</td>\n",
- " <td>0</td>\n",
- " <td>d775daf03cf949c25340db800bb25f4eec3c5fda</td>\n",
+ " <td>795771</td>\n",
+ " <td>35</td>\n",
+ " <td>222</td>\n",
+ " <td>3b8e75d37adb9ba3951ec8b2aae85ba1fa9b02f1</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 20200811 AK 4589.0 286155.0 NaN 39.0 \n",
- "1 20200811 AL 103851.0 679838.0 NaN 1506.0 \n",
+ "0 20200812 AK 4655.0 287927.0 NaN 39.0 \n",
+ "1 20200812 AL 104786.0 690985.0 NaN 1372.0 \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 12070.0 NaN 1270.0 \n",
+ "1 12292.0 NaN 1282.0 \n",
"\n",
" onVentilatorCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 4.0 ... 290744 0 0 \n",
- "1 NaN ... 783689 50 0 \n",
+ "0 3.0 ... 292582 1 0 \n",
+ "1 NaN ... 795771 35 222 \n",
"\n",
" hash commercialScore \\\n",
- "0 75189f7e45df3d19bc61fc8790a6df68e33c41e4 0 \n",
- "1 d775daf03cf949c25340db800bb25f4eec3c5fda 0 \n",
+ "0 04d3f681722d466f15660e1ded53888693484520 0 \n",
+ "1 3b8e75d37adb9ba3951ec8b2aae85ba1fa9b02f1 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": 8.638524,
- "end_time": "2020-08-12T07:32:55.057745",
+ "duration": 5.465167,
+ "end_time": "2020-08-13T07:32:10.255042",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/fa34vlpr/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/8ktvuu43/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/fa34vlpr/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/8ktvuu43/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-08-12T07:32:46.419221",
+ "start_time": "2020-08-13T07:32:04.789875",
"version": "1.1.0"
}
},