diff --git a/.renku/workflow/131c8c06eb2a49a881e084d0059d2f4f.cwl b/.renku/workflow/131c8c06eb2a49a881e084d0059d2f4f.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..4dfcafb5b02a659a4997a1d338d99655b2e51278
--- /dev/null
+++ b/.renku/workflow/131c8c06eb2a49a881e084d0059d2f4f.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_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-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 8d53d0c2ab8d4154bf3ce4af71f21484697edd9e..94a719dc1de0d440bb6b1acb267ee79aa20fe040 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 sha256:51ad395a5bf2b0dde015a25045dd5d982591167b21bdbf99d72a51085935e0fe
-size 17895030
+oid sha256:3ff5d0b0ec9b68bbb55366451290acb3cda356cf65dc6488d418eadf86b99b7f
+size 17971928
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 2f4c82cc7503a4dba103f43a4460560059e5e553..f3ae311413814ef2aa58bfde815fbfdfad41d9ec 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 sha256:462decf550f00953608ce2ea38092635fbe8b563a67081eb916f96311be18acc
-size 102176
+oid sha256:9101103d33ef39bce2611514a520e30ad8d441db9e018bd050c4fc03ea735105
+size 102468
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 5784883f0bb6f2ef54d5baa57b610eb4c5ad7274..6c387fec3927115300e12162807457f74704820e 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": 3.550558,
- "end_time": "2020-10-25T07:37:45.875174",
+ "duration": 2.326882,
+ "end_time": "2020-10-26T07:37:39.549797",
"exception": false,
- "start_time": "2020-10-25T07:37:42.324616",
+ "start_time": "2020-10-26T07:37:37.222915",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.027824,
- "end_time": "2020-10-25T07:37:45.918328",
+ "duration": 0.021897,
+ "end_time": "2020-10-26T07:37:39.585932",
"exception": false,
- "start_time": "2020-10-25T07:37:45.890504",
+ "start_time": "2020-10-26T07:37:39.564035",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.027753,
- "end_time": "2020-10-25T07:37:45.960330",
+ "duration": 0.021802,
+ "end_time": "2020-10-26T07:37:39.618175",
"exception": false,
- "start_time": "2020-10-25T07:37:45.932577",
+ "start_time": "2020-10-26T07:37:39.596373",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/g156d8nk/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/nez13572/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": 0.007933,
- "end_time": "2020-10-25T07:37:45.980254",
+ "duration": 0.007886,
+ "end_time": "2020-10-26T07:37:39.636816",
"exception": false,
- "start_time": "2020-10-25T07:37:45.972321",
+ "start_time": "2020-10-26T07:37:39.628930",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.6145,
- "end_time": "2020-10-25T07:37:46.602858",
+ "duration": 0.632897,
+ "end_time": "2020-10-26T07:37:40.277250",
"exception": false,
- "start_time": "2020-10-25T07:37:45.988358",
+ "start_time": "2020-10-26T07:37:39.644353",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.019979,
- "end_time": "2020-10-25T07:37:46.634561",
+ "duration": 0.023332,
+ "end_time": "2020-10-26T07:37:40.311285",
"exception": false,
- "start_time": "2020-10-25T07:37:46.614582",
+ "start_time": "2020-10-26T07:37:40.287953",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.088566,
- "end_time": "2020-10-25T07:37:46.735021",
+ "duration": 0.101663,
+ "end_time": "2020-10-26T07:37:40.422853",
"exception": false,
- "start_time": "2020-10-25T07:37:46.646455",
+ "start_time": "2020-10-26T07:37:40.321190",
"status": "completed"
},
"tags": []
@@ -280,10 +280,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007662,
- "end_time": "2020-10-25T07:37:46.755490",
+ "duration": 0.00813,
+ "end_time": "2020-10-26T07:37:40.440587",
"exception": false,
- "start_time": "2020-10-25T07:37:46.747828",
+ "start_time": "2020-10-26T07:37:40.432457",
"status": "completed"
},
"tags": []
@@ -297,10 +297,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 29.73858,
- "end_time": "2020-10-25T07:38:16.502066",
+ "duration": 29.828599,
+ "end_time": "2020-10-26T07:38:10.278079",
"exception": false,
- "start_time": "2020-10-25T07:37:46.763486",
+ "start_time": "2020-10-26T07:37:40.449480",
"status": "completed"
},
"tags": []
@@ -317,10 +317,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.064526,
- "end_time": "2020-10-25T07:38:16.581680",
+ "duration": 0.060729,
+ "end_time": "2020-10-26T07:38:10.353261",
"exception": false,
- "start_time": "2020-10-25T07:38:16.517154",
+ "start_time": "2020-10-26T07:38:10.292532",
"status": "completed"
},
"tags": []
@@ -339,10 +339,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.658515,
- "end_time": "2020-10-25T07:38:17.252086",
+ "duration": 0.666286,
+ "end_time": "2020-10-26T07:38:11.030070",
"exception": false,
- "start_time": "2020-10-25T07:38:16.593571",
+ "start_time": "2020-10-26T07:38:10.363784",
"status": "completed"
},
"tags": []
@@ -352,7 +352,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "13157 data points\n"
+ "13213 data points\n"
]
},
{
@@ -402,21 +402,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201024</td>\n",
+ " <td>20201025</td>\n",
" <td>AK</td>\n",
- " <td>13535.0</td>\n",
+ " <td>14064.0</td>\n",
" <td>NaN</td>\n",
- " <td>539585.0</td>\n",
+ " <td>545905.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>552746.0</td>\n",
+ " <td>559969.0</td>\n",
" <td>58.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>553120</td>\n",
+ " <td>559969</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
- " <td>280ee400bd797c20b77218c9e54a0b6615f91a53</td>\n",
+ " <td>175a4f70a15c098ac277246bff6ae33838f66029</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>20201024</td>\n",
+ " <td>20201025</td>\n",
" <td>AL</td>\n",
- " <td>183276.0</td>\n",
- " <td>26330.0</td>\n",
- " <td>1138922.0</td>\n",
+ " <td>184355.0</td>\n",
+ " <td>26474.0</td>\n",
+ " <td>1144785.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1295868.0</td>\n",
- " <td>920.0</td>\n",
+ " <td>1302666.0</td>\n",
+ " <td>922.0</td>\n",
" <td>19595.0</td>\n",
" <td>...</td>\n",
- " <td>1322198</td>\n",
- " <td>7</td>\n",
+ " <td>1329140</td>\n",
" <td>0</td>\n",
- " <td>7c16e74ce103ea23b8b2ef6881fc773d44d21f55</td>\n",
+ " <td>0</td>\n",
+ " <td>14421edcbba78df1217731644f92a3a03211c44d</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 20201024 AK 13535.0 NaN 539585.0 NaN \n",
- "1 20201024 AL 183276.0 26330.0 1138922.0 NaN \n",
+ "0 20201025 AK 14064.0 NaN 545905.0 NaN \n",
+ "1 20201025 AL 184355.0 26474.0 1144785.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 552746.0 58.0 \n",
- "1 totalTestsViral 1295868.0 920.0 \n",
+ "0 totalTestsViral 559969.0 58.0 \n",
+ "1 totalTestsViral 1302666.0 922.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 NaN ... 553120 0 0 \n",
- "1 19595.0 ... 1322198 7 0 \n",
+ "0 NaN ... 559969 0 0 \n",
+ "1 19595.0 ... 1329140 0 0 \n",
"\n",
" hash commercialScore \\\n",
- "0 280ee400bd797c20b77218c9e54a0b6615f91a53 0 \n",
- "1 7c16e74ce103ea23b8b2ef6881fc773d44d21f55 0 \n",
+ "0 175a4f70a15c098ac277246bff6ae33838f66029 0 \n",
+ "1 14421edcbba78df1217731644f92a3a03211c44d 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": 36.766249,
- "end_time": "2020-10-25T07:38:17.574642",
+ "duration": 35.451391,
+ "end_time": "2020-10-26T07:38:11.351400",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/g156d8nk/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/nez13572/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/g156d8nk/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/nez13572/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-10-25T07:37:40.808393",
+ "start_time": "2020-10-26T07:37:35.900009",
"version": "1.1.0"
}
},