diff --git a/.renku/workflow/ec866df5f2c0429ca86f04829489e0b0.cwl b/.renku/workflow/ec866df5f2c0429ca86f04829489e0b0.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..4dd78826e1abf9a4aee255083a983b5e736fe094
--- /dev/null
+++ b/.renku/workflow/ec866df5f2c0429ca86f04829489e0b0.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: states-daily.json
+ streamable: false
+ type: string
+ input_3:
+ default: out_folder
+ streamable: false
+ type: string
+ input_4:
+ default: data/covidtracking
+ streamable: false
+ type: string
+ input_5:
+ default:
+ class: File
+ path: ../../notebooks/process/download-covidtracking-data.ipynb
+ streamable: false
+ type: File
+ input_6:
+ default: runs/download-covidtracking-data.runs.ipynb
+ streamable: false
+ type: string
+outputs:
+ output_0:
+ outputSource: step_3/output_1
+ streamable: false
+ type: Directory
+ output_3:
+ outputSource: step_3/output_0
+ streamable: false
+ type: File
+requirements: []
+steps:
+ step_1:
+ in:
+ filename: input_1
+ input_directory: step_3/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:
+ filename: input_2
+ input_directory: step_3/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: []
+ step_3:
+ in:
+ input_1: input_3
+ input_2: input_4
+ input_3: input_5
+ input_4: input_6
+ out:
+ - output_0
+ - output_1
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index 6dd10404fcaf8e8605e0ee12aef3000125ea7a40..b24a82eabb5b0aa649b2221efebad0a4006c571f 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 sha256:1db64bf05ba50bd7a87d3ac5ec39cbdffabac74019e66066ad6d869f7a961ea0
-size 6818612
+oid sha256:07d8fb27d4370ea29687e03981bd732cfbf647dbd1aed89256d1a4e489ab49c7
+size 6871224
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 3fc6339f8e675720db62256fd26449bf198b286e..04e820843efef880c4eb84cffea4a56cc6c06423 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 sha256:6d6512ed1bdfcac4a24fa5fccbdf9b06e76d9187eb6a707766831fc7589382ca
-size 48897
+oid sha256:45a2572bd641eeac8a4bda332023f0fc319b6507dc49b3fb819bc85897f9c65e
+size 49640
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 8caf4186af28774fd4aca1c7b4a8832cc8a40bcd..4aae90d032e087a4d8fa5b84645f8af43a496307 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": 2.265336,
- "end_time": "2020-07-15T07:31:11.645868",
+ "duration": 5.211328,
+ "end_time": "2020-07-16T07:36:32.349184",
"exception": false,
- "start_time": "2020-07-15T07:31:09.380532",
+ "start_time": "2020-07-16T07:36:27.137856",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.021481,
- "end_time": "2020-07-15T07:31:11.681445",
+ "duration": 0.020238,
+ "end_time": "2020-07-16T07:36:32.380757",
"exception": false,
- "start_time": "2020-07-15T07:31:11.659964",
+ "start_time": "2020-07-16T07:36:32.360519",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.025026,
- "end_time": "2020-07-15T07:31:11.715032",
+ "duration": 0.020212,
+ "end_time": "2020-07-16T07:36:32.412094",
"exception": false,
- "start_time": "2020-07-15T07:31:11.690006",
+ "start_time": "2020-07-16T07:36:32.391882",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/5hekzgtt/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/z5hwmmrn/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": 0.007207,
- "end_time": "2020-07-15T07:31:11.734576",
+ "duration": 0.009151,
+ "end_time": "2020-07-16T07:36:32.432210",
"exception": false,
- "start_time": "2020-07-15T07:31:11.727369",
+ "start_time": "2020-07-16T07:36:32.423059",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.094813,
- "end_time": "2020-07-15T07:31:11.835983",
+ "duration": 0.193284,
+ "end_time": "2020-07-16T07:36:32.634328",
"exception": false,
- "start_time": "2020-07-15T07:31:11.741170",
+ "start_time": "2020-07-16T07:36:32.441044",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.023474,
- "end_time": "2020-07-15T07:31:11.867961",
+ "duration": 0.021824,
+ "end_time": "2020-07-16T07:36:32.667175",
"exception": false,
- "start_time": "2020-07-15T07:31:11.844487",
+ "start_time": "2020-07-16T07:36:32.645351",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.078157,
- "end_time": "2020-07-15T07:31:11.953010",
+ "duration": 0.071576,
+ "end_time": "2020-07-16T07:36:32.749621",
"exception": false,
- "start_time": "2020-07-15T07:31:11.874853",
+ "start_time": "2020-07-16T07:36:32.678045",
"status": "completed"
},
"tags": []
@@ -249,10 +249,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.009274,
- "end_time": "2020-07-15T07:31:11.974426",
+ "duration": 0.008642,
+ "end_time": "2020-07-16T07:36:32.769476",
"exception": false,
- "start_time": "2020-07-15T07:31:11.965152",
+ "start_time": "2020-07-16T07:36:32.760834",
"status": "completed"
},
"tags": []
@@ -266,10 +266,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.260704,
- "end_time": "2020-07-15T07:31:12.243305",
+ "duration": 0.308814,
+ "end_time": "2020-07-16T07:36:33.087074",
"exception": false,
- "start_time": "2020-07-15T07:31:11.982601",
+ "start_time": "2020-07-16T07:36:32.778260",
"status": "completed"
},
"tags": []
@@ -286,10 +286,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.037799,
- "end_time": "2020-07-15T07:31:12.298355",
+ "duration": 0.0299,
+ "end_time": "2020-07-16T07:36:33.129622",
"exception": false,
- "start_time": "2020-07-15T07:31:12.260556",
+ "start_time": "2020-07-16T07:36:33.099722",
"status": "completed"
},
"tags": []
@@ -308,10 +308,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.29273,
- "end_time": "2020-07-15T07:31:12.605093",
+ "duration": 0.274984,
+ "end_time": "2020-07-16T07:36:33.418558",
"exception": false,
- "start_time": "2020-07-15T07:31:12.312363",
+ "start_time": "2020-07-16T07:36:33.143574",
"status": "completed"
},
"tags": []
@@ -321,7 +321,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "7353 data points\n"
+ "7409 data points\n"
]
},
{
@@ -371,21 +371,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200714</td>\n",
+ " <td>20200715</td>\n",
" <td>AK</td>\n",
- " <td>1579.0</td>\n",
- " <td>147894.0</td>\n",
+ " <td>1631.0</td>\n",
+ " <td>154462.0</td>\n",
" <td>NaN</td>\n",
- " <td>25.0</td>\n",
+ " <td>32.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>1.0</td>\n",
+ " <td>0.0</td>\n",
" <td>...</td>\n",
- " <td>149473</td>\n",
+ " <td>156093</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
- " <td>14ec620d73185257a210b3f634cca1a8024dabe0</td>\n",
+ " <td>94f51a21cc1532dde7387df47013f567fb56d967</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>20200714</td>\n",
+ " <td>20200715</td>\n",
" <td>AL</td>\n",
- " <td>57255.0</td>\n",
- " <td>471834.0</td>\n",
+ " <td>59067.0</td>\n",
+ " <td>481982.0</td>\n",
" <td>NaN</td>\n",
- " <td>1353.0</td>\n",
- " <td>7123.0</td>\n",
+ " <td>1362.0</td>\n",
+ " <td>7291.0</td>\n",
" <td>NaN</td>\n",
- " <td>931.0</td>\n",
+ " <td>941.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>529089</td>\n",
- " <td>40</td>\n",
- " <td>378</td>\n",
- " <td>820cd0cab43d1d4994f54d9f80d70d3ce3257dbe</td>\n",
+ " <td>541049</td>\n",
+ " <td>47</td>\n",
+ " <td>168</td>\n",
+ " <td>115a76b81b0c3c59d334b5de8180c2e10899dddc</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 20200714 AK 1579.0 147894.0 NaN 25.0 \n",
- "1 20200714 AL 57255.0 471834.0 NaN 1353.0 \n",
+ "0 20200715 AK 1631.0 154462.0 NaN 32.0 \n",
+ "1 20200715 AL 59067.0 481982.0 NaN 1362.0 \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 7123.0 NaN 931.0 \n",
+ "1 7291.0 NaN 941.0 \n",
"\n",
" onVentilatorCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 1.0 ... 149473 0 0 \n",
- "1 NaN ... 529089 40 378 \n",
+ "0 0.0 ... 156093 0 0 \n",
+ "1 NaN ... 541049 47 168 \n",
"\n",
" hash commercialScore \\\n",
- "0 14ec620d73185257a210b3f634cca1a8024dabe0 0 \n",
- "1 820cd0cab43d1d4994f54d9f80d70d3ce3257dbe 0 \n",
+ "0 94f51a21cc1532dde7387df47013f567fb56d967 0 \n",
+ "1 115a76b81b0c3c59d334b5de8180c2e10899dddc 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": 5.225562,
- "end_time": "2020-07-15T07:31:12.927967",
+ "duration": 8.748295,
+ "end_time": "2020-07-16T07:36:33.741465",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/5hekzgtt/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/z5hwmmrn/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/5hekzgtt/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/z5hwmmrn/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-07-15T07:31:07.702405",
+ "start_time": "2020-07-16T07:36:24.993170",
"version": "1.1.0"
}
},