diff --git a/.renku/workflow/483e40a495904a2288be9d726c9b92c5.cwl b/.renku/workflow/483e40a495904a2288be9d726c9b92c5.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..e54b728802b5744f8b8054606ce39610d9874558
--- /dev/null
+++ b/.renku/workflow/483e40a495904a2288be9d726c9b92c5.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: states-metadata.json
+ streamable: false
+ type: string
+ input_3:
+ default: out_folder
+ streamable: false
+ type: string
+ input_4:
+ default: data/covidtracking
+ streamable: false
+ type: string
+ input_5:
+ default:
+ class: File
+ path: ../../notebooks/process/download-covidtracking-data.ipynb
+ streamable: false
+ type: File
+ input_6:
+ default: runs/download-covidtracking-data.runs.ipynb
+ streamable: false
+ type: string
+outputs:
+ output_1:
+ outputSource: step_3/output_0
+ streamable: false
+ type: File
+ output_2:
+ outputSource: step_3/output_1
+ streamable: false
+ type: Directory
+requirements: []
+steps:
+ step_1:
+ in:
+ filename: input_1
+ input_directory: step_3/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:
+ filename: input_2
+ input_directory: step_3/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: []
+ step_3:
+ in:
+ input_1: input_3
+ input_2: input_4
+ input_3: input_5
+ input_4: input_6
+ out:
+ - output_1
+ - output_0
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index c5739f4821e7ab286eda5168ad968fa52f205ef0..8d6811d28b2d933b59350c6f7d2152356dbdfbc6 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 sha256:6b23b6cdfea63f363d0244e4e1859d75ba4baddfbe7f1571703225f3c68e02b3
-size 20871740
+oid sha256:b3870e9d0d8671ee96a4b67b4ae3cb88150570b12b4920ac00eeccd59d0434fa
+size 20948510
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 22b5c42cfaf33f8bb64c1978277bc3407aee9342..448071e9eda65b0c600e44dd3c2f4edc83caf6dc 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:f1e8c29c1e07a6a0a43ab820487798e34d9fb582ef24f67153d777a8b4968071
-size 139663
+oid sha256:4dfdebe6042c969cd79cd09a220b6041e51b3536d57b674454d6e272a7b38d89
+size 141310
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 8f4574412e1113ee4b631eade1398b6dffb3d0a1..d98fa25f796156222639e6d0509b2e446490fdf1 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": 4.756697,
- "end_time": "2020-12-01T07:37:01.782160",
+ "duration": 3.93015,
+ "end_time": "2020-12-02T07:37:54.293969",
"exception": false,
- "start_time": "2020-12-01T07:36:57.025463",
+ "start_time": "2020-12-02T07:37:50.363819",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.020999,
- "end_time": "2020-12-01T07:37:01.816589",
+ "duration": 0.021148,
+ "end_time": "2020-12-02T07:37:54.329512",
"exception": false,
- "start_time": "2020-12-01T07:37:01.795590",
+ "start_time": "2020-12-02T07:37:54.308364",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.019808,
- "end_time": "2020-12-01T07:37:01.844709",
+ "duration": 0.01668,
+ "end_time": "2020-12-02T07:37:54.353751",
"exception": false,
- "start_time": "2020-12-01T07:37:01.824901",
+ "start_time": "2020-12-02T07:37:54.337071",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/c1zx9gql/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/0vxtf18s/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": 0.00769,
- "end_time": "2020-12-01T07:37:01.860374",
+ "duration": 0.005936,
+ "end_time": "2020-12-02T07:37:54.365726",
"exception": false,
- "start_time": "2020-12-01T07:37:01.852684",
+ "start_time": "2020-12-02T07:37:54.359790",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.335211,
- "end_time": "2020-12-01T07:37:02.201150",
+ "duration": 0.458783,
+ "end_time": "2020-12-02T07:37:54.829423",
"exception": false,
- "start_time": "2020-12-01T07:37:01.865939",
+ "start_time": "2020-12-02T07:37:54.370640",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.025666,
- "end_time": "2020-12-01T07:37:02.240440",
+ "duration": 0.022083,
+ "end_time": "2020-12-02T07:37:54.864086",
"exception": false,
- "start_time": "2020-12-01T07:37:02.214774",
+ "start_time": "2020-12-02T07:37:54.842003",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.069108,
- "end_time": "2020-12-01T07:37:02.314783",
+ "duration": 0.066974,
+ "end_time": "2020-12-02T07:37:54.940047",
"exception": false,
- "start_time": "2020-12-01T07:37:02.245675",
+ "start_time": "2020-12-02T07:37:54.873073",
"status": "completed"
},
"tags": []
@@ -284,10 +284,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007566,
- "end_time": "2020-12-01T07:37:02.334631",
+ "duration": 0.007203,
+ "end_time": "2020-12-02T07:37:54.959979",
"exception": false,
- "start_time": "2020-12-01T07:37:02.327065",
+ "start_time": "2020-12-02T07:37:54.952776",
"status": "completed"
},
"tags": []
@@ -301,10 +301,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.672308,
- "end_time": "2020-12-01T07:37:03.012521",
+ "duration": 0.62676,
+ "end_time": "2020-12-02T07:37:55.592981",
"exception": false,
- "start_time": "2020-12-01T07:37:02.340213",
+ "start_time": "2020-12-02T07:37:54.966221",
"status": "completed"
},
"tags": []
@@ -321,10 +321,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.048797,
- "end_time": "2020-12-01T07:37:03.078266",
+ "duration": 0.043914,
+ "end_time": "2020-12-02T07:37:55.652028",
"exception": false,
- "start_time": "2020-12-01T07:37:03.029469",
+ "start_time": "2020-12-02T07:37:55.608114",
"status": "completed"
},
"tags": []
@@ -343,10 +343,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.560952,
- "end_time": "2020-12-01T07:37:03.651492",
+ "duration": 0.517154,
+ "end_time": "2020-12-02T07:37:56.182763",
"exception": false,
- "start_time": "2020-12-01T07:37:03.090540",
+ "start_time": "2020-12-02T07:37:55.665609",
"status": "completed"
},
"tags": []
@@ -356,7 +356,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "15297 data points\n"
+ "15353 data points\n"
]
},
{
@@ -406,21 +406,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201130</td>\n",
+ " <td>20201201</td>\n",
" <td>AK</td>\n",
- " <td>31323.0</td>\n",
+ " <td>31834.0</td>\n",
" <td>NaN</td>\n",
- " <td>980073.0</td>\n",
+ " <td>986794.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1011396.0</td>\n",
- " <td>162.0</td>\n",
- " <td>725.0</td>\n",
+ " <td>1018628.0</td>\n",
+ " <td>155.0</td>\n",
+ " <td>749.0</td>\n",
" <td>...</td>\n",
- " <td>1011396</td>\n",
- " <td>0</td>\n",
- " <td>3</td>\n",
- " <td>271d3c383c856d19d56e16fbd4efca0f728d6f5a</td>\n",
+ " <td>1018628</td>\n",
+ " <td>1</td>\n",
+ " <td>24</td>\n",
+ " <td>6c0d9dbaedf0d16c7d345f9928e37ce2dba3a0ec</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>20201130</td>\n",
+ " <td>20201201</td>\n",
" <td>AL</td>\n",
- " <td>249524.0</td>\n",
- " <td>41501.0</td>\n",
- " <td>1376324.0</td>\n",
+ " <td>252900.0</td>\n",
+ " <td>42863.0</td>\n",
+ " <td>1383805.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1584347.0</td>\n",
- " <td>1717.0</td>\n",
- " <td>25338.0</td>\n",
+ " <td>1593842.0</td>\n",
+ " <td>1785.0</td>\n",
+ " <td>25610.0</td>\n",
" <td>...</td>\n",
- " <td>1625848</td>\n",
- " <td>1</td>\n",
- " <td>668</td>\n",
- " <td>1d4953d87fd314f6eb3ff436b379ce3b6ff4fab7</td>\n",
+ " <td>1636705</td>\n",
+ " <td>60</td>\n",
+ " <td>272</td>\n",
+ " <td>ff146d1c2df88ca7b0ac8e94dacc310424c5f0ba</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 20201130 AK 31323.0 NaN 980073.0 NaN \n",
- "1 20201130 AL 249524.0 41501.0 1376324.0 NaN \n",
+ "0 20201201 AK 31834.0 NaN 986794.0 NaN \n",
+ "1 20201201 AL 252900.0 42863.0 1383805.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 1011396.0 162.0 \n",
- "1 totalTestsViral 1584347.0 1717.0 \n",
+ "0 totalTestsViral 1018628.0 155.0 \n",
+ "1 totalTestsViral 1593842.0 1785.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 725.0 ... 1011396 0 3 \n",
- "1 25338.0 ... 1625848 1 668 \n",
+ "0 749.0 ... 1018628 1 24 \n",
+ "1 25610.0 ... 1636705 60 272 \n",
"\n",
" hash commercialScore \\\n",
- "0 271d3c383c856d19d56e16fbd4efca0f728d6f5a 0 \n",
- "1 1d4953d87fd314f6eb3ff436b379ce3b6ff4fab7 0 \n",
+ "0 6c0d9dbaedf0d16c7d345f9928e37ce2dba3a0ec 0 \n",
+ "1 ff146d1c2df88ca7b0ac8e94dacc310424c5f0ba 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": 8.757211,
- "end_time": "2020-12-01T07:37:03.973005",
+ "duration": 8.024748,
+ "end_time": "2020-12-02T07:37:56.505279",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/c1zx9gql/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/0vxtf18s/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/c1zx9gql/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/0vxtf18s/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-12-01T07:36:55.215794",
+ "start_time": "2020-12-02T07:37:48.480531",
"version": "1.1.0"
}
},