diff --git a/.renku/workflow/7d6191ace0bd4c75bfa6debfc195b857.cwl b/.renku/workflow/7d6191ace0bd4c75bfa6debfc195b857.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..4954d051a85321c882c22370c097db11e7654adc
--- /dev/null
+++ b/.renku/workflow/7d6191ace0bd4c75bfa6debfc195b857.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_0:
+ outputSource: step_1/output_0
+ streamable: false
+ type: File
+ output_2:
+ 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_0
+ - output_1
+ 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 3b31fd5e4dfc8f0a58bdec607bab3e20f01b7739..a6c08f854787af8fbe4082a9a01c2f1a51e6a8d0 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 sha256:40c4e7c36a3a3edadce9aa9741dca93fda9bb696d41ffe83157f69afc1a45604
-size 18459097
+oid sha256:62d83a9e7e219b75a90a189b1afb7bc9b6bf64b0c1640f0a71d25ac2395c0017
+size 18536189
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index dd134035858a3a69df7aa93fad234bc9bf26480c..e377d225be631104357677458ab4407b6e03fb34 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:bb5e9f61edebb173aea0a7c02035ee98d39365bd0b3fb95c513697e502342668
-size 108377
+oid sha256:e5c9982f4d81279d78cee5958a09ef5197dde0a9ac1d96cc2cb456bf4629da9d
+size 108379
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 9a3388ebb4868c0c9b3fa1525cc670a1e9d37220..014eaa71d48963607ccf2f7efd7ccbdb2f261827 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": 3.682234,
- "end_time": "2020-10-31T07:41:00.543129",
+ "duration": 5.037062,
+ "end_time": "2020-11-01T07:37:45.933708",
"exception": false,
- "start_time": "2020-10-31T07:40:56.860895",
+ "start_time": "2020-11-01T07:37:40.896646",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.024558,
- "end_time": "2020-10-31T07:41:00.583002",
+ "duration": 0.02828,
+ "end_time": "2020-11-01T07:37:45.978315",
"exception": false,
- "start_time": "2020-10-31T07:41:00.558444",
+ "start_time": "2020-11-01T07:37:45.950035",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.019837,
- "end_time": "2020-10-31T07:41:00.610773",
+ "duration": 0.022512,
+ "end_time": "2020-11-01T07:37:46.013706",
"exception": false,
- "start_time": "2020-10-31T07:41:00.590936",
+ "start_time": "2020-11-01T07:37:45.991194",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/5go_iu__/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/y_sxckx7/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": 0.006231,
- "end_time": "2020-10-31T07:41:00.624248",
+ "duration": 0.006401,
+ "end_time": "2020-11-01T07:37:46.029106",
"exception": false,
- "start_time": "2020-10-31T07:41:00.618017",
+ "start_time": "2020-11-01T07:37:46.022705",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.859229,
- "end_time": "2020-10-31T07:41:01.488799",
+ "duration": 0.65798,
+ "end_time": "2020-11-01T07:37:46.693110",
"exception": false,
- "start_time": "2020-10-31T07:41:00.629570",
+ "start_time": "2020-11-01T07:37:46.035130",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.030144,
- "end_time": "2020-10-31T07:41:01.534355",
+ "duration": 0.028713,
+ "end_time": "2020-11-01T07:37:46.735011",
"exception": false,
- "start_time": "2020-10-31T07:41:01.504211",
+ "start_time": "2020-11-01T07:37:46.706298",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.099661,
- "end_time": "2020-10-31T07:41:01.644716",
+ "duration": 0.090248,
+ "end_time": "2020-11-01T07:37:46.838574",
"exception": false,
- "start_time": "2020-10-31T07:41:01.545055",
+ "start_time": "2020-11-01T07:37:46.748326",
"status": "completed"
},
"tags": []
@@ -280,10 +280,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007944,
- "end_time": "2020-10-31T07:41:01.667560",
+ "duration": 0.007958,
+ "end_time": "2020-11-01T07:37:46.859707",
"exception": false,
- "start_time": "2020-10-31T07:41:01.659616",
+ "start_time": "2020-11-01T07:37:46.851749",
"status": "completed"
},
"tags": []
@@ -297,10 +297,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 30.643978,
- "end_time": "2020-10-31T07:41:32.318512",
+ "duration": 0.437219,
+ "end_time": "2020-11-01T07:37:47.303780",
"exception": false,
- "start_time": "2020-10-31T07:41:01.674534",
+ "start_time": "2020-11-01T07:37:46.866561",
"status": "completed"
},
"tags": []
@@ -317,10 +317,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.054579,
- "end_time": "2020-10-31T07:41:32.390496",
+ "duration": 0.063124,
+ "end_time": "2020-11-01T07:37:47.378855",
"exception": false,
- "start_time": "2020-10-31T07:41:32.335917",
+ "start_time": "2020-11-01T07:37:47.315731",
"status": "completed"
},
"tags": []
@@ -339,10 +339,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.594878,
- "end_time": "2020-10-31T07:41:33.000128",
+ "duration": 0.650152,
+ "end_time": "2020-11-01T07:37:48.043379",
"exception": false,
- "start_time": "2020-10-31T07:41:32.405250",
+ "start_time": "2020-11-01T07:37:47.393227",
"status": "completed"
},
"tags": []
@@ -352,7 +352,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "13551 data points\n"
+ "13607 data points\n"
]
},
{
@@ -402,21 +402,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201030</td>\n",
+ " <td>20201031</td>\n",
" <td>AK</td>\n",
- " <td>15908.0</td>\n",
+ " <td>16355.0</td>\n",
" <td>NaN</td>\n",
- " <td>570415.0</td>\n",
+ " <td>587852.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>586323.0</td>\n",
- " <td>90.0</td>\n",
+ " <td>604207.0</td>\n",
+ " <td>94.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>586323</td>\n",
- " <td>4</td>\n",
+ " <td>604207</td>\n",
+ " <td>1</td>\n",
" <td>0</td>\n",
- " <td>f02fcc28ab30329793653f2d5759c257699cb0de</td>\n",
+ " <td>4fd1e9352fd403f75cd0f4b8c7d420de8eb73f0b</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>20201030</td>\n",
+ " <td>20201031</td>\n",
" <td>AL</td>\n",
- " <td>190496.0</td>\n",
- " <td>27776.0</td>\n",
- " <td>1172969.0</td>\n",
+ " <td>192285.0</td>\n",
+ " <td>27990.0</td>\n",
+ " <td>1181958.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1335689.0</td>\n",
- " <td>1013.0</td>\n",
+ " <td>1346253.0</td>\n",
+ " <td>960.0</td>\n",
" <td>20450.0</td>\n",
" <td>...</td>\n",
- " <td>1363465</td>\n",
- " <td>18</td>\n",
- " <td>204</td>\n",
- " <td>2731923ac8ca3480f0dfe4eb973a4345f06e5643</td>\n",
+ " <td>1374243</td>\n",
+ " <td>35</td>\n",
+ " <td>0</td>\n",
+ " <td>5194e1ea04ad4dace9ab68daca52f9fa98e39f1b</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 20201030 AK 15908.0 NaN 570415.0 NaN \n",
- "1 20201030 AL 190496.0 27776.0 1172969.0 NaN \n",
+ "0 20201031 AK 16355.0 NaN 587852.0 NaN \n",
+ "1 20201031 AL 192285.0 27990.0 1181958.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 586323.0 90.0 \n",
- "1 totalTestsViral 1335689.0 1013.0 \n",
+ "0 totalTestsViral 604207.0 94.0 \n",
+ "1 totalTestsViral 1346253.0 960.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 NaN ... 586323 4 0 \n",
- "1 20450.0 ... 1363465 18 204 \n",
+ "0 NaN ... 604207 1 0 \n",
+ "1 20450.0 ... 1374243 35 0 \n",
"\n",
" hash commercialScore \\\n",
- "0 f02fcc28ab30329793653f2d5759c257699cb0de 0 \n",
- "1 2731923ac8ca3480f0dfe4eb973a4345f06e5643 0 \n",
+ "0 4fd1e9352fd403f75cd0f4b8c7d420de8eb73f0b 0 \n",
+ "1 5194e1ea04ad4dace9ab68daca52f9fa98e39f1b 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": 38.867596,
- "end_time": "2020-10-31T07:41:33.426697",
+ "duration": 9.337475,
+ "end_time": "2020-11-01T07:37:48.472569",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/5go_iu__/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/y_sxckx7/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/5go_iu__/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/y_sxckx7/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-10-31T07:40:54.559101",
+ "start_time": "2020-11-01T07:37:39.135094",
"version": "1.1.0"
}
},