diff --git a/.renku/workflow/fbace511124b4e699b2f666805684da3.cwl b/.renku/workflow/fbace511124b4e699b2f666805684da3.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..5f28111f52f4637b8db4fd3a68ed32e5df4855aa
--- /dev/null
+++ b/.renku/workflow/fbace511124b4e699b2f666805684da3.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_3:
+ 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_1
+ - output_0
+ 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 9a83b6ddb5b0dc3c148c4df09edfa1b69a00c1f8..c5739f4821e7ab286eda5168ad968fa52f205ef0 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 sha256:4343f9d15b80f8d128d38cf2c74618f97bfa72464bc5404202538b6eb7387241
-size 20794411
+oid sha256:6b23b6cdfea63f363d0244e4e1859d75ba4baddfbe7f1571703225f3c68e02b3
+size 20871740
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index aaeb4ec13732b880127cedfbab4f7410df8d49bf..22b5c42cfaf33f8bb64c1978277bc3407aee9342 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:dee9012019c64b770d4edecdf24be64226b3caaa9f272ba0d98e076e095ba64f
-size 138920
+oid sha256:f1e8c29c1e07a6a0a43ab820487798e34d9fb582ef24f67153d777a8b4968071
+size 139663
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index e5a39760e2e0dd889af54044e53fdb30541a2ff9..8f4574412e1113ee4b631eade1398b6dffb3d0a1 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": 7.254927,
- "end_time": "2020-11-30T07:42:25.992308",
+ "duration": 4.756697,
+ "end_time": "2020-12-01T07:37:01.782160",
"exception": false,
- "start_time": "2020-11-30T07:42:18.737381",
+ "start_time": "2020-12-01T07:36:57.025463",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.02438,
- "end_time": "2020-11-30T07:42:26.029562",
+ "duration": 0.020999,
+ "end_time": "2020-12-01T07:37:01.816589",
"exception": false,
- "start_time": "2020-11-30T07:42:26.005182",
+ "start_time": "2020-12-01T07:37:01.795590",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.019627,
- "end_time": "2020-11-30T07:42:26.055405",
+ "duration": 0.019808,
+ "end_time": "2020-12-01T07:37:01.844709",
"exception": false,
- "start_time": "2020-11-30T07:42:26.035778",
+ "start_time": "2020-12-01T07:37:01.824901",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/nfpct0h_/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/c1zx9gql/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": 0.010253,
- "end_time": "2020-11-30T07:42:26.074463",
+ "duration": 0.00769,
+ "end_time": "2020-12-01T07:37:01.860374",
"exception": false,
- "start_time": "2020-11-30T07:42:26.064210",
+ "start_time": "2020-12-01T07:37:01.852684",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.984019,
- "end_time": "2020-11-30T07:42:27.064920",
+ "duration": 0.335211,
+ "end_time": "2020-12-01T07:37:02.201150",
"exception": false,
- "start_time": "2020-11-30T07:42:26.080901",
+ "start_time": "2020-12-01T07:37:01.865939",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.026879,
- "end_time": "2020-11-30T07:42:27.098307",
+ "duration": 0.025666,
+ "end_time": "2020-12-01T07:37:02.240440",
"exception": false,
- "start_time": "2020-11-30T07:42:27.071428",
+ "start_time": "2020-12-01T07:37:02.214774",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.092631,
- "end_time": "2020-11-30T07:42:27.201746",
+ "duration": 0.069108,
+ "end_time": "2020-12-01T07:37:02.314783",
"exception": false,
- "start_time": "2020-11-30T07:42:27.109115",
+ "start_time": "2020-12-01T07:37:02.245675",
"status": "completed"
},
"tags": []
@@ -284,10 +284,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.009333,
- "end_time": "2020-11-30T07:42:27.223510",
+ "duration": 0.007566,
+ "end_time": "2020-12-01T07:37:02.334631",
"exception": false,
- "start_time": "2020-11-30T07:42:27.214177",
+ "start_time": "2020-12-01T07:37:02.327065",
"status": "completed"
},
"tags": []
@@ -301,10 +301,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 34.7292,
- "end_time": "2020-11-30T07:43:01.959865",
+ "duration": 0.672308,
+ "end_time": "2020-12-01T07:37:03.012521",
"exception": false,
- "start_time": "2020-11-30T07:42:27.230665",
+ "start_time": "2020-12-01T07:37:02.340213",
"status": "completed"
},
"tags": []
@@ -321,10 +321,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.048863,
- "end_time": "2020-11-30T07:43:02.021438",
+ "duration": 0.048797,
+ "end_time": "2020-12-01T07:37:03.078266",
"exception": false,
- "start_time": "2020-11-30T07:43:01.972575",
+ "start_time": "2020-12-01T07:37:03.029469",
"status": "completed"
},
"tags": []
@@ -343,10 +343,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.859792,
- "end_time": "2020-11-30T07:43:05.217727",
+ "duration": 0.560952,
+ "end_time": "2020-12-01T07:37:03.651492",
"exception": false,
- "start_time": "2020-11-30T07:43:04.357935",
+ "start_time": "2020-12-01T07:37:03.090540",
"status": "completed"
},
"tags": []
@@ -356,7 +356,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "15241 data points\n"
+ "15297 data points\n"
]
},
{
@@ -406,21 +406,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201129</td>\n",
+ " <td>20201130</td>\n",
" <td>AK</td>\n",
- " <td>30816.0</td>\n",
+ " <td>31323.0</td>\n",
" <td>NaN</td>\n",
- " <td>975364.0</td>\n",
+ " <td>980073.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1006180.0</td>\n",
- " <td>159.0</td>\n",
- " <td>722.0</td>\n",
+ " <td>1011396.0</td>\n",
+ " <td>162.0</td>\n",
+ " <td>725.0</td>\n",
" <td>...</td>\n",
- " <td>1006180</td>\n",
+ " <td>1011396</td>\n",
" <td>0</td>\n",
- " <td>1</td>\n",
- " <td>81a1922227c01f54d1d8cc7e718af55ee8b6804b</td>\n",
+ " <td>3</td>\n",
+ " <td>271d3c383c856d19d56e16fbd4efca0f728d6f5a</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -430,21 +430,21 @@
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20201129</td>\n",
+ " <td>20201130</td>\n",
" <td>AL</td>\n",
- " <td>247229.0</td>\n",
- " <td>41286.0</td>\n",
- " <td>1373770.0</td>\n",
+ " <td>249524.0</td>\n",
+ " <td>41501.0</td>\n",
+ " <td>1376324.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1579713.0</td>\n",
- " <td>1609.0</td>\n",
- " <td>24670.0</td>\n",
+ " <td>1584347.0</td>\n",
+ " <td>1717.0</td>\n",
+ " <td>25338.0</td>\n",
" <td>...</td>\n",
- " <td>1620999</td>\n",
- " <td>5</td>\n",
- " <td>0</td>\n",
- " <td>c6fbe324336aa11a724d65ccedc8971e5509bb4e</td>\n",
+ " <td>1625848</td>\n",
+ " <td>1</td>\n",
+ " <td>668</td>\n",
+ " <td>1d4953d87fd314f6eb3ff436b379ce3b6ff4fab7</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -459,20 +459,20 @@
],
"text/plain": [
" date state positive probableCases negative pending \\\n",
- "0 20201129 AK 30816.0 NaN 975364.0 NaN \n",
- "1 20201129 AL 247229.0 41286.0 1373770.0 NaN \n",
+ "0 20201130 AK 31323.0 NaN 980073.0 NaN \n",
+ "1 20201130 AL 249524.0 41501.0 1376324.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 1006180.0 159.0 \n",
- "1 totalTestsViral 1579713.0 1609.0 \n",
+ "0 totalTestsViral 1011396.0 162.0 \n",
+ "1 totalTestsViral 1584347.0 1717.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 722.0 ... 1006180 0 1 \n",
- "1 24670.0 ... 1620999 5 0 \n",
+ "0 725.0 ... 1011396 0 3 \n",
+ "1 25338.0 ... 1625848 1 668 \n",
"\n",
" hash commercialScore \\\n",
- "0 81a1922227c01f54d1d8cc7e718af55ee8b6804b 0 \n",
- "1 c6fbe324336aa11a724d65ccedc8971e5509bb4e 0 \n",
+ "0 271d3c383c856d19d56e16fbd4efca0f728d6f5a 0 \n",
+ "1 1d4953d87fd314f6eb3ff436b379ce3b6ff4fab7 0 \n",
"\n",
" negativeRegularScore negativeScore positiveScore score grade \n",
"0 0 0 0 0 \n",
@@ -512,18 +512,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 49.469852,
- "end_time": "2020-11-30T07:43:05.649715",
+ "duration": 8.757211,
+ "end_time": "2020-12-01T07:37:03.973005",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/nfpct0h_/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/c1zx9gql/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/nfpct0h_/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/c1zx9gql/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-11-30T07:42:16.179863",
+ "start_time": "2020-12-01T07:36:55.215794",
"version": "1.1.0"
}
},