diff --git a/.renku/workflow/01af5e5b09a643b296080a4480511bcf.cwl b/.renku/workflow/01af5e5b09a643b296080a4480511bcf.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..0a5677d4c0f7cf03ea8c89762667ca5696448c94
--- /dev/null
+++ b/.renku/workflow/01af5e5b09a643b296080a4480511bcf.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-metadata.json
+ streamable: false
+ type: string
+ input_6:
+ default: states-daily.json
+ streamable: false
+ type: string
+outputs:
+ output_0:
+ outputSource: step_1/output_0
+ streamable: false
+ type: File
+ output_3:
+ outputSource: step_1/output_1
+ streamable: false
+ type: Directory
+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-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_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-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 1cd6df0ddedbbd52536a66c68860e85e003511f6..6723798333d1d196fc2e3c122a502d2b4f12aa11 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:de3dec44cc02cf27d1490d8740874950610ef254879ef4e8df9597e6cb1e4647
-size 19692962
+oid sha256:581b2d97d6ae787294c5c3764d6b4803343504cde2d509b8751e70777de4427b
+size 19769722
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 336cae1af43a1c182653d11f551dce12d1fb5a13..0f95736a243bef0bcd994e289776436e69eca25c 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 sha256:1901716d1e6321bf5b177b779b8a4857b0c35fe61e24a53d7a37c9a3513988b0
-size 121791
+oid sha256:ad5953bf232f30a978fd9915c9e87610ace47f93da17b8fd009fcd1c6480f69c
+size 123062
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index d47258686586b06ccea0f48a88c3947598b48342..137ea109f754078bd09fdaaa0974de00b7996d90 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": 5.531971,
- "end_time": "2020-11-16T07:36:41.614756",
+ "duration": 5.032173,
+ "end_time": "2020-11-17T07:42:42.936102",
"exception": false,
- "start_time": "2020-11-16T07:36:36.082785",
+ "start_time": "2020-11-17T07:42:37.903929",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.018945,
- "end_time": "2020-11-16T07:36:41.648956",
+ "duration": 0.029006,
+ "end_time": "2020-11-17T07:42:42.981669",
"exception": false,
- "start_time": "2020-11-16T07:36:41.630011",
+ "start_time": "2020-11-17T07:42:42.952663",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.011935,
- "end_time": "2020-11-16T07:36:41.668692",
+ "duration": 0.026,
+ "end_time": "2020-11-17T07:42:43.021237",
"exception": false,
- "start_time": "2020-11-16T07:36:41.656757",
+ "start_time": "2020-11-17T07:42:42.995237",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/8a0rjkgq/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/nu8t6zmk/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": 0.0049,
- "end_time": "2020-11-16T07:36:41.677826",
+ "duration": 0.007143,
+ "end_time": "2020-11-17T07:42:43.039079",
"exception": false,
- "start_time": "2020-11-16T07:36:41.672926",
+ "start_time": "2020-11-17T07:42:43.031936",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.390166,
- "end_time": "2020-11-16T07:36:42.072559",
+ "duration": 0.399521,
+ "end_time": "2020-11-17T07:42:43.444673",
"exception": false,
- "start_time": "2020-11-16T07:36:41.682393",
+ "start_time": "2020-11-17T07:42:43.045152",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.022204,
- "end_time": "2020-11-16T07:36:42.107795",
+ "duration": 0.028097,
+ "end_time": "2020-11-17T07:42:43.488259",
"exception": false,
- "start_time": "2020-11-16T07:36:42.085591",
+ "start_time": "2020-11-17T07:42:43.460162",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.064797,
- "end_time": "2020-11-16T07:36:42.179830",
+ "duration": 0.10648,
+ "end_time": "2020-11-17T07:42:43.604236",
"exception": false,
- "start_time": "2020-11-16T07:36:42.115033",
+ "start_time": "2020-11-17T07:42:43.497756",
"status": "completed"
},
"tags": []
@@ -284,10 +284,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.00734,
- "end_time": "2020-11-16T07:36:42.199365",
+ "duration": 0.007903,
+ "end_time": "2020-11-17T07:42:43.625221",
"exception": false,
- "start_time": "2020-11-16T07:36:42.192025",
+ "start_time": "2020-11-17T07:42:43.617318",
"status": "completed"
},
"tags": []
@@ -301,10 +301,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.441262,
- "end_time": "2020-11-16T07:36:42.646845",
+ "duration": 0.649363,
+ "end_time": "2020-11-17T07:42:44.280699",
"exception": false,
- "start_time": "2020-11-16T07:36:42.205583",
+ "start_time": "2020-11-17T07:42:43.631336",
"status": "completed"
},
"tags": []
@@ -321,10 +321,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.167171,
- "end_time": "2020-11-16T07:36:42.829617",
+ "duration": 0.055423,
+ "end_time": "2020-11-17T07:42:44.355421",
"exception": false,
- "start_time": "2020-11-16T07:36:42.662446",
+ "start_time": "2020-11-17T07:42:44.299998",
"status": "completed"
},
"tags": []
@@ -343,10 +343,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.568847,
- "end_time": "2020-11-16T07:36:43.413261",
+ "duration": 0.811442,
+ "end_time": "2020-11-17T07:42:45.181932",
"exception": false,
- "start_time": "2020-11-16T07:36:42.844414",
+ "start_time": "2020-11-17T07:42:44.370490",
"status": "completed"
},
"tags": []
@@ -356,7 +356,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "14447 data points\n"
+ "14503 data points\n"
]
},
{
@@ -406,21 +406,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201115</td>\n",
+ " <td>20201116</td>\n",
" <td>AK</td>\n",
- " <td>23814.0</td>\n",
+ " <td>23240.0</td>\n",
" <td>NaN</td>\n",
- " <td>843568.0</td>\n",
+ " <td>849107.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>867382.0</td>\n",
- " <td>141.0</td>\n",
- " <td>NaN</td>\n",
+ " <td>872347.0</td>\n",
+ " <td>143.0</td>\n",
+ " <td>559.0</td>\n",
" <td>...</td>\n",
- " <td>867382</td>\n",
- " <td>0</td>\n",
+ " <td>872347</td>\n",
" <td>0</td>\n",
- " <td>e932ee5bb80cf68522ff67db8d19bd8e6e3f3c1c</td>\n",
+ " <td>9</td>\n",
+ " <td>f9555880eaacb39588e3dbdc1822f7fca35ebf82</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>20201115</td>\n",
+ " <td>20201116</td>\n",
" <td>AL</td>\n",
- " <td>217822.0</td>\n",
- " <td>34331.0</td>\n",
- " <td>1275915.0</td>\n",
+ " <td>219232.0</td>\n",
+ " <td>34587.0</td>\n",
+ " <td>1281958.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1459406.0</td>\n",
- " <td>1195.0</td>\n",
- " <td>22275.0</td>\n",
+ " <td>1466603.0</td>\n",
+ " <td>1262.0</td>\n",
+ " <td>22716.0</td>\n",
" <td>...</td>\n",
- " <td>1493737</td>\n",
- " <td>2</td>\n",
- " <td>0</td>\n",
- " <td>bd0aca6268151786d8349818e098840bf0ce6a42</td>\n",
+ " <td>1501190</td>\n",
+ " <td>1</td>\n",
+ " <td>441</td>\n",
+ " <td>6a3bed8bae24c6fd056a322cdf8bdb75b8e91348</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 20201115 AK 23814.0 NaN 843568.0 NaN \n",
- "1 20201115 AL 217822.0 34331.0 1275915.0 NaN \n",
+ "0 20201116 AK 23240.0 NaN 849107.0 NaN \n",
+ "1 20201116 AL 219232.0 34587.0 1281958.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 867382.0 141.0 \n",
- "1 totalTestsViral 1459406.0 1195.0 \n",
+ "0 totalTestsViral 872347.0 143.0 \n",
+ "1 totalTestsViral 1466603.0 1262.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 NaN ... 867382 0 0 \n",
- "1 22275.0 ... 1493737 2 0 \n",
+ "0 559.0 ... 872347 0 9 \n",
+ "1 22716.0 ... 1501190 1 441 \n",
"\n",
" hash commercialScore \\\n",
- "0 e932ee5bb80cf68522ff67db8d19bd8e6e3f3c1c 0 \n",
- "1 bd0aca6268151786d8349818e098840bf0ce6a42 0 \n",
+ "0 f9555880eaacb39588e3dbdc1822f7fca35ebf82 0 \n",
+ "1 6a3bed8bae24c6fd056a322cdf8bdb75b8e91348 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": 9.282661,
- "end_time": "2020-11-16T07:36:43.734701",
+ "duration": 9.728724,
+ "end_time": "2020-11-17T07:42:45.610567",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/8a0rjkgq/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/nu8t6zmk/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/8a0rjkgq/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/nu8t6zmk/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-11-16T07:36:34.452040",
+ "start_time": "2020-11-17T07:42:35.881843",
"version": "1.1.0"
}
},