diff --git a/.renku/workflow/050e8f458e484c0281c4846de954afc4.cwl b/.renku/workflow/050e8f458e484c0281c4846de954afc4.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..a0067321b319ba052a8214144f686dadf2c8ec12
--- /dev/null
+++ b/.renku/workflow/050e8f458e484c0281c4846de954afc4.cwl
@@ -0,0 +1,120 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: states-daily.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-metadata.json
+ streamable: false
+ type: string
+outputs:
+ output_1:
+ outputSource: step_2/output_1
+ streamable: false
+ type: Directory
+ output_2:
+ 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-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_2:
+ in:
+ input_1: input_2
+ input_2: input_3
+ input_3: input_4
+ input_4: input_5
+ out:
+ - output_1
+ - output_0
+ 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-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 89e38926d251824a8368c05303803c7cbfb33a96..305d9455a5e79f4eccfeab6a9c4946c71008a9af 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 sha256:2ed324b60f9234bd8aac0bf8bb578d96458dddd114bd13441a39ca9a958d660b
-size 18844434
+oid sha256:43110b45fbcaf372e87ef2da0578a7738d41ab1ef43c88163f61b52cd26d0c8f
+size 18921545
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index e804187c31ca72ae796a0b5e6b1ff34a4a826577..cb98443aaed7f2b829f385f7e5c8d25e64c9e317 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 sha256:64019b2ea484dda369afd8063c139dbd29e791776e41a66cda0c4e36adaa2ae4
-size 110301
+oid sha256:3856ce65b8cdf051d3887ddb14a1fed8c0ca94fa3028146ea446348f9ad7eec0
+size 112431
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index bdad21c41e32e363a655a00b6b8b0e4e3d3de556..b0388faba7dbf1839ae0a8d498f2bad54faa9a25 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": 6.729895,
- "end_time": "2020-11-05T07:38:41.062106",
+ "duration": 4.567062,
+ "end_time": "2020-11-06T07:36:16.535139",
"exception": false,
- "start_time": "2020-11-05T07:38:34.332211",
+ "start_time": "2020-11-06T07:36:11.968077",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.024761,
- "end_time": "2020-11-05T07:38:41.103587",
+ "duration": 0.021675,
+ "end_time": "2020-11-06T07:36:16.571363",
"exception": false,
- "start_time": "2020-11-05T07:38:41.078826",
+ "start_time": "2020-11-06T07:36:16.549688",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.026788,
- "end_time": "2020-11-05T07:38:41.142628",
+ "duration": 0.016527,
+ "end_time": "2020-11-06T07:36:16.595797",
"exception": false,
- "start_time": "2020-11-05T07:38:41.115840",
+ "start_time": "2020-11-06T07:36:16.579270",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/vbj6b6ni/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/cvg3ldzb/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": 0.009469,
- "end_time": "2020-11-05T07:38:41.167225",
+ "duration": 0.004867,
+ "end_time": "2020-11-06T07:36:16.605495",
"exception": false,
- "start_time": "2020-11-05T07:38:41.157756",
+ "start_time": "2020-11-06T07:36:16.600628",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.242981,
- "end_time": "2020-11-05T07:38:41.417207",
+ "duration": 0.679735,
+ "end_time": "2020-11-06T07:36:17.289998",
"exception": false,
- "start_time": "2020-11-05T07:38:41.174226",
+ "start_time": "2020-11-06T07:36:16.610263",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.030029,
- "end_time": "2020-11-05T07:38:41.462901",
+ "duration": 0.022148,
+ "end_time": "2020-11-06T07:36:17.323825",
"exception": false,
- "start_time": "2020-11-05T07:38:41.432872",
+ "start_time": "2020-11-06T07:36:17.301677",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.111829,
- "end_time": "2020-11-05T07:38:41.587925",
+ "duration": 0.124039,
+ "end_time": "2020-11-06T07:36:17.456351",
"exception": false,
- "start_time": "2020-11-05T07:38:41.476096",
+ "start_time": "2020-11-06T07:36:17.332312",
"status": "completed"
},
"tags": []
@@ -280,10 +280,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007981,
- "end_time": "2020-11-05T07:38:41.608573",
+ "duration": 0.006929,
+ "end_time": "2020-11-06T07:36:17.474962",
"exception": false,
- "start_time": "2020-11-05T07:38:41.600592",
+ "start_time": "2020-11-06T07:36:17.468033",
"status": "completed"
},
"tags": []
@@ -297,10 +297,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.452865,
- "end_time": "2020-11-05T07:38:42.068098",
+ "duration": 0.608193,
+ "end_time": "2020-11-06T07:36:18.089165",
"exception": false,
- "start_time": "2020-11-05T07:38:41.615233",
+ "start_time": "2020-11-06T07:36:17.480972",
"status": "completed"
},
"tags": []
@@ -317,10 +317,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.049196,
- "end_time": "2020-11-05T07:38:42.134677",
+ "duration": 0.041932,
+ "end_time": "2020-11-06T07:36:18.146875",
"exception": false,
- "start_time": "2020-11-05T07:38:42.085481",
+ "start_time": "2020-11-06T07:36:18.104943",
"status": "completed"
},
"tags": []
@@ -339,10 +339,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.643402,
- "end_time": "2020-11-05T07:38:42.793243",
+ "duration": 0.55035,
+ "end_time": "2020-11-06T07:36:18.711417",
"exception": false,
- "start_time": "2020-11-05T07:38:42.149841",
+ "start_time": "2020-11-06T07:36:18.161067",
"status": "completed"
},
"tags": []
@@ -352,7 +352,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "13831 data points\n"
+ "13887 data points\n"
]
},
{
@@ -402,21 +402,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201104</td>\n",
+ " <td>20201105</td>\n",
" <td>AK</td>\n",
- " <td>17860.0</td>\n",
+ " <td>18174.0</td>\n",
" <td>NaN</td>\n",
- " <td>609898.0</td>\n",
+ " <td>763652.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>627758.0</td>\n",
- " <td>95.0</td>\n",
+ " <td>781826.0</td>\n",
+ " <td>104.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>627758</td>\n",
+ " <td>781826</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
- " <td>b1f3faafdb8100fd0d67eb31a3614c20da9f076c</td>\n",
+ " <td>910e0e68ec1831715444823aa43d30e203d4ec90</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -426,21 +426,21 @@
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20201104</td>\n",
+ " <td>20201105</td>\n",
" <td>AL</td>\n",
- " <td>197777.0</td>\n",
- " <td>29662.0</td>\n",
- " <td>1203497.0</td>\n",
+ " <td>199158.0</td>\n",
+ " <td>29892.0</td>\n",
+ " <td>1209841.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1371612.0</td>\n",
- " <td>1017.0</td>\n",
+ " <td>1379107.0</td>\n",
+ " <td>994.0</td>\n",
" <td>21027.0</td>\n",
" <td>...</td>\n",
- " <td>1401274</td>\n",
- " <td>19</td>\n",
- " <td>126</td>\n",
- " <td>1bac7f8b3ff7ab5f7136284a077b2ab1fd62cc5b</td>\n",
+ " <td>1408999</td>\n",
+ " <td>20</td>\n",
+ " <td>0</td>\n",
+ " <td>e660184b515c15867ae651a03b8c7f2f23271e52</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -455,20 +455,20 @@
],
"text/plain": [
" date state positive probableCases negative pending \\\n",
- "0 20201104 AK 17860.0 NaN 609898.0 NaN \n",
- "1 20201104 AL 197777.0 29662.0 1203497.0 NaN \n",
+ "0 20201105 AK 18174.0 NaN 763652.0 NaN \n",
+ "1 20201105 AL 199158.0 29892.0 1209841.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 627758.0 95.0 \n",
- "1 totalTestsViral 1371612.0 1017.0 \n",
+ "0 totalTestsViral 781826.0 104.0 \n",
+ "1 totalTestsViral 1379107.0 994.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 NaN ... 627758 0 0 \n",
- "1 21027.0 ... 1401274 19 126 \n",
+ "0 NaN ... 781826 0 0 \n",
+ "1 21027.0 ... 1408999 20 0 \n",
"\n",
" hash commercialScore \\\n",
- "0 b1f3faafdb8100fd0d67eb31a3614c20da9f076c 0 \n",
- "1 1bac7f8b3ff7ab5f7136284a077b2ab1fd62cc5b 0 \n",
+ "0 910e0e68ec1831715444823aa43d30e203d4ec90 0 \n",
+ "1 e660184b515c15867ae651a03b8c7f2f23271e52 0 \n",
"\n",
" negativeRegularScore negativeScore positiveScore score grade \n",
"0 0 0 0 0 \n",
@@ -508,18 +508,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 10.85433,
- "end_time": "2020-11-05T07:38:43.223805",
+ "duration": 8.490223,
+ "end_time": "2020-11-06T07:36:19.033810",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/vbj6b6ni/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/cvg3ldzb/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/vbj6b6ni/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/cvg3ldzb/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-11-05T07:38:32.369475",
+ "start_time": "2020-11-06T07:36:10.543587",
"version": "1.1.0"
}
},