diff --git a/.renku/workflow/0a1ea867681b42e9babe7bd954cfcf54.cwl b/.renku/workflow/0a1ea867681b42e9babe7bd954cfcf54.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..de4a095f84fb3800ed9630517dbdb7ee9f0e874e
--- /dev/null
+++ b/.renku/workflow/0a1ea867681b42e9babe7bd954cfcf54.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_1:
+ outputSource: step_1/output_1
+ streamable: false
+ type: Directory
+ output_2:
+ 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 b7b4847ba1fc445c41ad9cefbd5ab923ee49ece2..48da09c3cbff59e3e01fea220c41b8a7ccfdc2ad 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 sha256:55e31693954feaa2fb9bba61bd6b30f7f119ea0a7a3e4f18aefe5a72af9f351c
-size 14455457
+oid sha256:6136c9676e800850762ab1152701a61382c92f61980841d108c11146a29bd9b1
+size 14530788
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 43665ea41ceef9f53ea9e7a1b9211f439a5bbed5..271a33c1d66a1d3bf89f2121cec04da72d703dca 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 sha256:0eecaefae3f2ed9046e67a913a9b6710d1bad97fd6fd0a48ab23d019b8139875
-size 73696
+oid sha256:99b0108722e9576f5d6a8d806819357999bb461cbc13f575db5c366bfbba325d
+size 74414
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index f6347310470a4d161f97809f6ced7c468811d367..29dcbdf6d75b542965bbb2436ca4ffacf7d5a738 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": 0.690894,
- "end_time": "2020-09-14T07:33:41.550115",
+ "duration": 3.758726,
+ "end_time": "2020-09-15T07:34:48.490913",
"exception": false,
- "start_time": "2020-09-14T07:33:40.859221",
+ "start_time": "2020-09-15T07:34:44.732187",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.022162,
- "end_time": "2020-09-14T07:33:41.581043",
+ "duration": 0.029344,
+ "end_time": "2020-09-15T07:34:48.536522",
"exception": false,
- "start_time": "2020-09-14T07:33:41.558881",
+ "start_time": "2020-09-15T07:34:48.507178",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.01904,
- "end_time": "2020-09-14T07:33:41.609092",
+ "duration": 0.033826,
+ "end_time": "2020-09-15T07:34:48.580975",
"exception": false,
- "start_time": "2020-09-14T07:33:41.590052",
+ "start_time": "2020-09-15T07:34:48.547149",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/oten11on/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/jsxpi5jx/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": 0.008436,
- "end_time": "2020-09-14T07:33:41.626207",
+ "duration": 0.010067,
+ "end_time": "2020-09-15T07:34:48.605607",
"exception": false,
- "start_time": "2020-09-14T07:33:41.617771",
+ "start_time": "2020-09-15T07:34:48.595540",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.608125,
- "end_time": "2020-09-14T07:33:42.241688",
+ "duration": 0.82058,
+ "end_time": "2020-09-15T07:34:49.433425",
"exception": false,
- "start_time": "2020-09-14T07:33:41.633563",
+ "start_time": "2020-09-15T07:34:48.612845",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.021432,
- "end_time": "2020-09-14T07:33:42.272317",
+ "duration": 0.027218,
+ "end_time": "2020-09-15T07:34:49.474403",
"exception": false,
- "start_time": "2020-09-14T07:33:42.250885",
+ "start_time": "2020-09-15T07:34:49.447185",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.075222,
- "end_time": "2020-09-14T07:33:42.356873",
+ "duration": 0.094807,
+ "end_time": "2020-09-15T07:34:49.578347",
"exception": false,
- "start_time": "2020-09-14T07:33:42.281651",
+ "start_time": "2020-09-15T07:34:49.483540",
"status": "completed"
},
"tags": []
@@ -263,10 +263,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008149,
- "end_time": "2020-09-14T07:33:42.374696",
+ "duration": 0.007654,
+ "end_time": "2020-09-15T07:34:49.599510",
"exception": false,
- "start_time": "2020-09-14T07:33:42.366547",
+ "start_time": "2020-09-15T07:34:49.591856",
"status": "completed"
},
"tags": []
@@ -280,10 +280,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 24.154098,
- "end_time": "2020-09-14T07:34:06.537107",
+ "duration": 24.500853,
+ "end_time": "2020-09-15T07:35:14.107416",
"exception": false,
- "start_time": "2020-09-14T07:33:42.383009",
+ "start_time": "2020-09-15T07:34:49.606563",
"status": "completed"
},
"tags": []
@@ -300,10 +300,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.038108,
- "end_time": "2020-09-14T07:34:06.584415",
+ "duration": 0.052058,
+ "end_time": "2020-09-15T07:35:14.175197",
"exception": false,
- "start_time": "2020-09-14T07:34:06.546307",
+ "start_time": "2020-09-15T07:35:14.123139",
"status": "completed"
},
"tags": []
@@ -322,10 +322,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.561879,
- "end_time": "2020-09-14T07:34:07.158624",
+ "duration": 0.515353,
+ "end_time": "2020-09-15T07:35:14.706843",
"exception": false,
- "start_time": "2020-09-14T07:34:06.596745",
+ "start_time": "2020-09-15T07:35:14.191490",
"status": "completed"
},
"tags": []
@@ -335,7 +335,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "10850 data points\n"
+ "10906 data points\n"
]
},
{
@@ -385,21 +385,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200913</td>\n",
+ " <td>20200914</td>\n",
" <td>AK</td>\n",
- " <td>7193.0</td>\n",
- " <td>394020.0</td>\n",
+ " <td>7270.0</td>\n",
+ " <td>396143.0</td>\n",
" <td>NaN</td>\n",
- " <td>35.0</td>\n",
+ " <td>37.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>8.0</td>\n",
" <td>...</td>\n",
- " <td>401213</td>\n",
+ " <td>403413</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
- " <td>f467ac0e20900a51da5e02bc4fb53260331b017c</td>\n",
+ " <td>c47ba6fdd7b2d5856a69b861c773b64ba0dfcb76</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -409,21 +409,21 @@
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200913</td>\n",
+ " <td>20200914</td>\n",
" <td>AL</td>\n",
- " <td>138755.0</td>\n",
- " <td>884432.0</td>\n",
+ " <td>139459.0</td>\n",
+ " <td>888092.0</td>\n",
" <td>NaN</td>\n",
- " <td>790.0</td>\n",
- " <td>15527.0</td>\n",
+ " <td>792.0</td>\n",
+ " <td>15756.0</td>\n",
" <td>NaN</td>\n",
- " <td>1610.0</td>\n",
+ " <td>1611.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>1023187</td>\n",
- " <td>1</td>\n",
- " <td>0</td>\n",
- " <td>b84d1499d4e7dde4dca550ed4ab983ad7a428a9e</td>\n",
+ " <td>1027551</td>\n",
+ " <td>4</td>\n",
+ " <td>229</td>\n",
+ " <td>a852a907f21a1d2ec711d522217d2fa536b912e5</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -438,20 +438,20 @@
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200913 AK 7193.0 394020.0 NaN 35.0 \n",
- "1 20200913 AL 138755.0 884432.0 NaN 790.0 \n",
+ "0 20200914 AK 7270.0 396143.0 NaN 37.0 \n",
+ "1 20200914 AL 139459.0 888092.0 NaN 792.0 \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 15527.0 NaN 1610.0 \n",
+ "1 15756.0 NaN 1611.0 \n",
"\n",
" onVentilatorCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 8.0 ... 401213 0 0 \n",
- "1 NaN ... 1023187 1 0 \n",
+ "0 8.0 ... 403413 0 0 \n",
+ "1 NaN ... 1027551 4 229 \n",
"\n",
" hash commercialScore \\\n",
- "0 f467ac0e20900a51da5e02bc4fb53260331b017c 0 \n",
- "1 b84d1499d4e7dde4dca550ed4ab983ad7a428a9e 0 \n",
+ "0 c47ba6fdd7b2d5856a69b861c773b64ba0dfcb76 0 \n",
+ "1 a852a907f21a1d2ec711d522217d2fa536b912e5 0 \n",
"\n",
" negativeRegularScore negativeScore positiveScore score grade \n",
"0 0 0 0 0 \n",
@@ -491,18 +491,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 27.930839,
- "end_time": "2020-09-14T07:34:07.581638",
+ "duration": 32.417203,
+ "end_time": "2020-09-15T07:35:15.138903",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/oten11on/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/jsxpi5jx/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/oten11on/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/jsxpi5jx/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-09-14T07:33:39.650799",
+ "start_time": "2020-09-15T07:34:42.721700",
"version": "1.1.0"
}
},