diff --git a/.renku/workflow/6cc6993066ed4a0b85d39713783f4d3c.cwl b/.renku/workflow/6cc6993066ed4a0b85d39713783f4d3c.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..83e33f7867f7684be36d1d03a70d01b8689f5d6d
--- /dev/null
+++ b/.renku/workflow/6cc6993066ed4a0b85d39713783f4d3c.cwl
@@ -0,0 +1,120 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: states-metadata.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-daily.json
+ streamable: false
+ type: string
+outputs:
+ output_2:
+ outputSource: step_2/output_1
+ streamable: false
+ type: Directory
+ output_3:
+ 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-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_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-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 088b3b2d51e067d613520d3aeb20273ef1866409..1075cc3f443cc14029bda3433ea3c838baba380e 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:a5c9838e8b91f25fe30aae1a2c60f3a12368ab033f914faf14f2d8df993633df
-size 1172128
+oid sha256:c80b65820b6241c370620a8583e079f6acafd8d9b421e5add6fc9d78220528d6
+size 1203304
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 947c0fec11f84d96a933abde803989339b9d04ee..8d90d68c4f7400ff9ed02bf524bde5ce8ad2448a 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 sha256:27fd69eb445fb8e3ce66f9d1ed73ebc72f24622cff7cbc37edc7651ebd4e331f
-size 27845
+oid sha256:a2e45292b5796ff458d826f6d1f26e8914d89ff5d87d78a5fb91c78f61237cc7
+size 27705
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index fc2535cb4331759a4756ad28d37fdc881b6b939e..b4cc7c18d3d49f7aada623e842f4508bd69b3cf5 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": 0.532269,
- "end_time": "2020-04-18T18:11:05.616063",
+ "duration": 5.671212,
+ "end_time": "2020-04-19T19:56:23.928932",
"exception": false,
- "start_time": "2020-04-18T18:11:05.083794",
+ "start_time": "2020-04-19T19:56:18.257720",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.018483,
- "end_time": "2020-04-18T18:11:05.645046",
+ "duration": 0.018453,
+ "end_time": "2020-04-19T19:56:23.958250",
"exception": false,
- "start_time": "2020-04-18T18:11:05.626563",
+ "start_time": "2020-04-19T19:56:23.939797",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.019301,
- "end_time": "2020-04-18T18:11:05.674172",
+ "duration": 0.019133,
+ "end_time": "2020-04-19T19:56:23.986818",
"exception": false,
- "start_time": "2020-04-18T18:11:05.654871",
+ "start_time": "2020-04-19T19:56:23.967685",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/lvwjkfpt/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/_uzn4el5/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": 0.007258,
- "end_time": "2020-04-18T18:11:05.690126",
+ "duration": 0.007776,
+ "end_time": "2020-04-19T19:56:24.002340",
"exception": false,
- "start_time": "2020-04-18T18:11:05.682868",
+ "start_time": "2020-04-19T19:56:23.994564",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.186003,
- "end_time": "2020-04-18T18:11:05.883651",
+ "duration": 0.160899,
+ "end_time": "2020-04-19T19:56:24.171242",
"exception": false,
- "start_time": "2020-04-18T18:11:05.697648",
+ "start_time": "2020-04-19T19:56:24.010343",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.022463,
- "end_time": "2020-04-18T18:11:05.916296",
+ "duration": 0.019485,
+ "end_time": "2020-04-19T19:56:24.199510",
"exception": false,
- "start_time": "2020-04-18T18:11:05.893833",
+ "start_time": "2020-04-19T19:56:24.180025",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.061515,
- "end_time": "2020-04-18T18:11:05.986966",
+ "duration": 0.085508,
+ "end_time": "2020-04-19T19:56:24.292339",
"exception": false,
- "start_time": "2020-04-18T18:11:05.925451",
+ "start_time": "2020-04-19T19:56:24.206831",
"status": "completed"
},
"tags": []
@@ -246,10 +246,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008277,
- "end_time": "2020-04-18T18:11:06.004318",
+ "duration": 0.008133,
+ "end_time": "2020-04-19T19:56:24.309427",
"exception": false,
- "start_time": "2020-04-18T18:11:05.996041",
+ "start_time": "2020-04-19T19:56:24.301294",
"status": "completed"
},
"tags": []
@@ -263,10 +263,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.160192,
- "end_time": "2020-04-18T18:11:06.172926",
+ "duration": 0.35078,
+ "end_time": "2020-04-19T19:56:24.668340",
"exception": false,
- "start_time": "2020-04-18T18:11:06.012734",
+ "start_time": "2020-04-19T19:56:24.317560",
"status": "completed"
},
"tags": []
@@ -283,10 +283,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.025967,
- "end_time": "2020-04-18T18:11:06.211115",
+ "duration": 0.022744,
+ "end_time": "2020-04-19T19:56:24.700667",
"exception": false,
- "start_time": "2020-04-18T18:11:06.185148",
+ "start_time": "2020-04-19T19:56:24.677923",
"status": "completed"
},
"tags": []
@@ -305,10 +305,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.111813,
- "end_time": "2020-04-18T18:11:06.335104",
+ "duration": 0.110746,
+ "end_time": "2020-04-19T19:56:24.819861",
"exception": false,
- "start_time": "2020-04-18T18:11:06.223291",
+ "start_time": "2020-04-19T19:56:24.709115",
"status": "completed"
},
"tags": []
@@ -318,7 +318,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "2396 data points\n"
+ "2452 data points\n"
]
},
{
@@ -368,51 +368,51 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200417</td>\n",
+ " <td>20200418</td>\n",
" <td>AK</td>\n",
- " <td>309.0</td>\n",
- " <td>9141.0</td>\n",
- " <td>NaN</td>\n",
+ " <td>314.0</td>\n",
+ " <td>9341.0</td>\n",
" <td>NaN</td>\n",
+ " <td>39.0</td>\n",
" <td>36.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
" <td>36.0</td>\n",
- " <td>9450.0</td>\n",
- " <td>9450.0</td>\n",
- " <td>9450.0</td>\n",
+ " <td>9655.0</td>\n",
+ " <td>9655.0</td>\n",
+ " <td>9655.0</td>\n",
" <td>2</td>\n",
" <td>0.0</td>\n",
- " <td>1.0</td>\n",
- " <td>706.0</td>\n",
- " <td>9.0</td>\n",
- " <td>715.0</td>\n",
+ " <td>0.0</td>\n",
+ " <td>200.0</td>\n",
+ " <td>5.0</td>\n",
+ " <td>205.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200417</td>\n",
+ " <td>20200418</td>\n",
" <td>AL</td>\n",
- " <td>4530.0</td>\n",
- " <td>33318.0</td>\n",
+ " <td>4655.0</td>\n",
+ " <td>37883.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>594.0</td>\n",
+ " <td>620.0</td>\n",
" <td>NaN</td>\n",
" <td>247.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>594.0</td>\n",
- " <td>37848.0</td>\n",
- " <td>37848.0</td>\n",
- " <td>37848.0</td>\n",
+ " <td>620.0</td>\n",
+ " <td>42538.0</td>\n",
+ " <td>42538.0</td>\n",
+ " <td>42538.0</td>\n",
" <td>1</td>\n",
- " <td>11.0</td>\n",
- " <td>41.0</td>\n",
- " <td>1272.0</td>\n",
- " <td>185.0</td>\n",
- " <td>1457.0</td>\n",
+ " <td>2.0</td>\n",
+ " <td>26.0</td>\n",
+ " <td>4565.0</td>\n",
+ " <td>125.0</td>\n",
+ " <td>4690.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
@@ -421,24 +421,24 @@
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200417 AK 309.0 9141.0 NaN NaN \n",
- "1 20200417 AL 4530.0 33318.0 NaN NaN \n",
+ "0 20200418 AK 314.0 9341.0 NaN 39.0 \n",
+ "1 20200418 AL 4655.0 37883.0 NaN NaN \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 36.0 NaN NaN \n",
- "1 594.0 NaN 247.0 \n",
+ "1 620.0 NaN 247.0 \n",
"\n",
" onVentilatorCurrently ... hospitalized total totalTestResults \\\n",
- "0 NaN ... 36.0 9450.0 9450.0 \n",
- "1 NaN ... 594.0 37848.0 37848.0 \n",
+ "0 NaN ... 36.0 9655.0 9655.0 \n",
+ "1 NaN ... 620.0 42538.0 42538.0 \n",
"\n",
" posNeg fips deathIncrease hospitalizedIncrease negativeIncrease \\\n",
- "0 9450.0 2 0.0 1.0 706.0 \n",
- "1 37848.0 1 11.0 41.0 1272.0 \n",
+ "0 9655.0 2 0.0 0.0 200.0 \n",
+ "1 42538.0 1 2.0 26.0 4565.0 \n",
"\n",
" positiveIncrease totalTestResultsIncrease \n",
- "0 9.0 715.0 \n",
- "1 185.0 1457.0 \n",
+ "0 5.0 205.0 \n",
+ "1 125.0 4690.0 \n",
"\n",
"[2 rows x 25 columns]"
]
@@ -474,18 +474,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 2.571431,
- "end_time": "2020-04-18T18:11:06.657430",
+ "duration": 8.208523,
+ "end_time": "2020-04-19T19:56:25.142083",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/lvwjkfpt/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/_uzn4el5/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/lvwjkfpt/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/_uzn4el5/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-04-18T18:11:04.085999",
+ "start_time": "2020-04-19T19:56:16.933560",
"version": "1.1.0"
}
},