diff --git a/.renku/workflow/95900e3b5544477fa36891fe80b71e6a.cwl b/.renku/workflow/95900e3b5544477fa36891fe80b71e6a.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..b611ac623c5d5e6d0474e0bbd43bb2fa2581deef
--- /dev/null
+++ b/.renku/workflow/95900e3b5544477fa36891fe80b71e6a.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_0:
+ outputSource: step_2/output_1
+ streamable: false
+ type: Directory
+ output_1:
+ outputSource: step_2/output_0
+ streamable: false
+ type: File
+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_0
+ - output_1
+ 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 451bde44e36499342a97eae629aec58f0f98a7b1..2f095ef2fd735027e9f3c9f814347edd3edc0852 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 sha256:0e93551218f4f81392d24f6ff17007b5121303ee9eb8dbc1559da7bec33c93b2
-size 7659954
+oid sha256:4a21497c9679604fb3a884b4621c552a77c070b108edf4d11427545366900bf5
+size 7712627
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index e561fa9622cfa022eda83539c390478cb223efc6..66087951a2b07b53031cc9d4ffe76fc1d9dfe823 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 sha256:97f32e3b08ceb5019605543e0a90d8b53c0933ad0950677c58fd868943bd2f38
-size 56338
+oid sha256:7bdcbea46addae2bd6392349d71b66545282603a1f4362689f95ef337a232937
+size 57221
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 9d0290c1e293d065698885606d17b3adc6af9559..66a52f842934a53ddcdeb638c118fb416e2d5dac 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": 0.636339,
- "end_time": "2020-07-31T07:31:38.916840",
+ "duration": 3.677738,
+ "end_time": "2020-08-01T07:32:36.765169",
"exception": false,
- "start_time": "2020-07-31T07:31:38.280501",
+ "start_time": "2020-08-01T07:32:33.087431",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.017811,
- "end_time": "2020-07-31T07:31:38.947335",
+ "duration": 0.024832,
+ "end_time": "2020-08-01T07:32:36.806906",
"exception": false,
- "start_time": "2020-07-31T07:31:38.929524",
+ "start_time": "2020-08-01T07:32:36.782074",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.019772,
- "end_time": "2020-07-31T07:31:38.974996",
+ "duration": 0.022172,
+ "end_time": "2020-08-01T07:32:36.839469",
"exception": false,
- "start_time": "2020-07-31T07:31:38.955224",
+ "start_time": "2020-08-01T07:32:36.817297",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/z_m8yogb/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/xpfpy1ny/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": 0.006274,
- "end_time": "2020-07-31T07:31:38.988972",
+ "duration": 0.00615,
+ "end_time": "2020-08-01T07:32:36.854666",
"exception": false,
- "start_time": "2020-07-31T07:31:38.982698",
+ "start_time": "2020-08-01T07:32:36.848516",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.31111,
- "end_time": "2020-07-31T07:31:39.306628",
+ "duration": 0.184244,
+ "end_time": "2020-08-01T07:32:37.044786",
"exception": false,
- "start_time": "2020-07-31T07:31:38.995518",
+ "start_time": "2020-08-01T07:32:36.860542",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.019968,
- "end_time": "2020-07-31T07:31:39.336696",
+ "duration": 0.032584,
+ "end_time": "2020-08-01T07:32:37.098311",
"exception": false,
- "start_time": "2020-07-31T07:31:39.316728",
+ "start_time": "2020-08-01T07:32:37.065727",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.058807,
- "end_time": "2020-07-31T07:31:39.403115",
+ "duration": 0.076098,
+ "end_time": "2020-08-01T07:32:37.188818",
"exception": false,
- "start_time": "2020-07-31T07:31:39.344308",
+ "start_time": "2020-08-01T07:32:37.112720",
"status": "completed"
},
"tags": []
@@ -249,10 +249,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007059,
- "end_time": "2020-07-31T07:31:39.417766",
+ "duration": 0.00836,
+ "end_time": "2020-08-01T07:32:37.211485",
"exception": false,
- "start_time": "2020-07-31T07:31:39.410707",
+ "start_time": "2020-08-01T07:32:37.203125",
"status": "completed"
},
"tags": []
@@ -266,10 +266,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.234612,
- "end_time": "2020-07-31T07:31:39.659826",
+ "duration": 0.24849,
+ "end_time": "2020-08-01T07:32:37.467781",
"exception": false,
- "start_time": "2020-07-31T07:31:39.425214",
+ "start_time": "2020-08-01T07:32:37.219291",
"status": "completed"
},
"tags": []
@@ -286,10 +286,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.029778,
- "end_time": "2020-07-31T07:31:39.701277",
+ "duration": 0.033347,
+ "end_time": "2020-08-01T07:32:37.518652",
"exception": false,
- "start_time": "2020-07-31T07:31:39.671499",
+ "start_time": "2020-08-01T07:32:37.485305",
"status": "completed"
},
"tags": []
@@ -308,10 +308,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.346106,
- "end_time": "2020-07-31T07:31:40.058722",
+ "duration": 0.307833,
+ "end_time": "2020-08-01T07:32:37.837752",
"exception": false,
- "start_time": "2020-07-31T07:31:39.712616",
+ "start_time": "2020-08-01T07:32:37.529919",
"status": "completed"
},
"tags": []
@@ -321,7 +321,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "8249 data points\n"
+ "8305 data points\n"
]
},
{
@@ -371,21 +371,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200730</td>\n",
+ " <td>20200731</td>\n",
" <td>AK</td>\n",
- " <td>3559.0</td>\n",
- " <td>221498.0</td>\n",
+ " <td>3677.0</td>\n",
+ " <td>229429.0</td>\n",
" <td>NaN</td>\n",
- " <td>45.0</td>\n",
+ " <td>40.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>3.0</td>\n",
" <td>...</td>\n",
- " <td>225057</td>\n",
- " <td>1</td>\n",
+ " <td>233106</td>\n",
+ " <td>0</td>\n",
" <td>0</td>\n",
- " <td>d66445af73028a02a5d6713580a4c470cc603322</td>\n",
+ " <td>435bc6d4686226ba3a508751129be8b2ef723836</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>20200730</td>\n",
+ " <td>20200731</td>\n",
" <td>AL</td>\n",
- " <td>85762.0</td>\n",
- " <td>594346.0</td>\n",
+ " <td>87723.0</td>\n",
+ " <td>601744.0</td>\n",
" <td>NaN</td>\n",
- " <td>1595.0</td>\n",
- " <td>10070.0</td>\n",
+ " <td>1596.0</td>\n",
+ " <td>10521.0</td>\n",
" <td>NaN</td>\n",
- " <td>1129.0</td>\n",
+ " <td>1144.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>680108</td>\n",
- " <td>27</td>\n",
- " <td>177</td>\n",
- " <td>5776f9724a3452e48705a9b2c73f52d3e631229d</td>\n",
+ " <td>689467</td>\n",
+ " <td>15</td>\n",
+ " <td>451</td>\n",
+ " <td>310a029041a6b87a179110674657ee90aac288c0</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 20200730 AK 3559.0 221498.0 NaN 45.0 \n",
- "1 20200730 AL 85762.0 594346.0 NaN 1595.0 \n",
+ "0 20200731 AK 3677.0 229429.0 NaN 40.0 \n",
+ "1 20200731 AL 87723.0 601744.0 NaN 1596.0 \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 10070.0 NaN 1129.0 \n",
+ "1 10521.0 NaN 1144.0 \n",
"\n",
" onVentilatorCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 3.0 ... 225057 1 0 \n",
- "1 NaN ... 680108 27 177 \n",
+ "0 3.0 ... 233106 0 0 \n",
+ "1 NaN ... 689467 15 451 \n",
"\n",
" hash commercialScore \\\n",
- "0 d66445af73028a02a5d6713580a4c470cc603322 0 \n",
- "1 5776f9724a3452e48705a9b2c73f52d3e631229d 0 \n",
+ "0 435bc6d4686226ba3a508751129be8b2ef723836 0 \n",
+ "1 310a029041a6b87a179110674657ee90aac288c0 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": 3.000062,
- "end_time": "2020-07-31T07:31:40.379070",
+ "duration": 6.732796,
+ "end_time": "2020-08-01T07:32:38.164781",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/z_m8yogb/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/xpfpy1ny/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/z_m8yogb/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/xpfpy1ny/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-07-31T07:31:37.379008",
+ "start_time": "2020-08-01T07:32:31.431985",
"version": "1.1.0"
}
},