diff --git a/.renku/workflow/65a9c0cbf9a7441a81ca03c877e1f779.cwl b/.renku/workflow/65a9c0cbf9a7441a81ca03c877e1f779.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..8518210df82611ec9385094956ad9049fb822354
--- /dev/null
+++ b/.renku/workflow/65a9c0cbf9a7441a81ca03c877e1f779.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: states-daily.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-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:
+ 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-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: []
+ step_3:
+ in:
+ input_1: input_3
+ input_2: input_4
+ input_3: input_5
+ input_4: input_6
+ out:
+ - output_0
+ - output_1
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index da8da07cbe24a8b1b67e26cd92295584f3f8e6b7..088b3b2d51e067d613520d3aeb20273ef1866409 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:e132f00c37bb95c13669d8ecb3f60036ea707c0f455ef7dd748dd3e9d7d6042e
-size 1140882
+oid sha256:a5c9838e8b91f25fe30aae1a2c60f3a12368ab033f914faf14f2d8df993633df
+size 1172128
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 6e194b2f4f7b3407811b1db1cfb392ce4d0466c1..947c0fec11f84d96a933abde803989339b9d04ee 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:a13c078a0a9faafb648501e3fc2fc589d75f9f689d9496c6129298a74e0334a1
-size 27965
+oid sha256:27fd69eb445fb8e3ce66f9d1ed73ebc72f24622cff7cbc37edc7651ebd4e331f
+size 27845
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 2baf2cd738a8649175ac1bceb5968bce7baedad6..fc2535cb4331759a4756ad28d37fdc881b6b939e 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": 2.580306,
- "end_time": "2020-04-17T07:25:14.828781",
+ "duration": 0.532269,
+ "end_time": "2020-04-18T18:11:05.616063",
"exception": false,
- "start_time": "2020-04-17T07:25:12.248475",
+ "start_time": "2020-04-18T18:11:05.083794",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.026104,
- "end_time": "2020-04-17T07:25:14.871596",
+ "duration": 0.018483,
+ "end_time": "2020-04-18T18:11:05.645046",
"exception": false,
- "start_time": "2020-04-17T07:25:14.845492",
+ "start_time": "2020-04-18T18:11:05.626563",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.026826,
- "end_time": "2020-04-17T07:25:14.911972",
+ "duration": 0.019301,
+ "end_time": "2020-04-18T18:11:05.674172",
"exception": false,
- "start_time": "2020-04-17T07:25:14.885146",
+ "start_time": "2020-04-18T18:11:05.654871",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/pnqb5z0q/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/lvwjkfpt/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": 0.007223,
- "end_time": "2020-04-17T07:25:14.929276",
+ "duration": 0.007258,
+ "end_time": "2020-04-18T18:11:05.690126",
"exception": false,
- "start_time": "2020-04-17T07:25:14.922053",
+ "start_time": "2020-04-18T18:11:05.682868",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.20702,
- "end_time": "2020-04-17T07:25:15.142890",
+ "duration": 0.186003,
+ "end_time": "2020-04-18T18:11:05.883651",
"exception": false,
- "start_time": "2020-04-17T07:25:14.935870",
+ "start_time": "2020-04-18T18:11:05.697648",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.024628,
- "end_time": "2020-04-17T07:25:15.178468",
+ "duration": 0.022463,
+ "end_time": "2020-04-18T18:11:05.916296",
"exception": false,
- "start_time": "2020-04-17T07:25:15.153840",
+ "start_time": "2020-04-18T18:11:05.893833",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.098225,
- "end_time": "2020-04-17T07:25:15.284990",
+ "duration": 0.061515,
+ "end_time": "2020-04-18T18:11:05.986966",
"exception": false,
- "start_time": "2020-04-17T07:25:15.186765",
+ "start_time": "2020-04-18T18:11:05.925451",
"status": "completed"
},
"tags": []
@@ -246,10 +246,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008857,
- "end_time": "2020-04-17T07:25:15.307561",
+ "duration": 0.008277,
+ "end_time": "2020-04-18T18:11:06.004318",
"exception": false,
- "start_time": "2020-04-17T07:25:15.298704",
+ "start_time": "2020-04-18T18:11:05.996041",
"status": "completed"
},
"tags": []
@@ -263,10 +263,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 1.815188,
- "end_time": "2020-04-17T07:25:17.129424",
+ "duration": 0.160192,
+ "end_time": "2020-04-18T18:11:06.172926",
"exception": false,
- "start_time": "2020-04-17T07:25:15.314236",
+ "start_time": "2020-04-18T18:11:06.012734",
"status": "completed"
},
"tags": []
@@ -283,10 +283,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.030238,
- "end_time": "2020-04-17T07:25:17.180355",
+ "duration": 0.025967,
+ "end_time": "2020-04-18T18:11:06.211115",
"exception": false,
- "start_time": "2020-04-17T07:25:17.150117",
+ "start_time": "2020-04-18T18:11:06.185148",
"status": "completed"
},
"tags": []
@@ -305,10 +305,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.1129,
- "end_time": "2020-04-17T07:25:17.305054",
+ "duration": 0.111813,
+ "end_time": "2020-04-18T18:11:06.335104",
"exception": false,
- "start_time": "2020-04-17T07:25:17.192154",
+ "start_time": "2020-04-18T18:11:06.223291",
"status": "completed"
},
"tags": []
@@ -318,7 +318,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "2340 data points\n"
+ "2396 data points\n"
]
},
{
@@ -368,51 +368,51 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200416</td>\n",
+ " <td>20200417</td>\n",
" <td>AK</td>\n",
- " <td>300.0</td>\n",
- " <td>8435.0</td>\n",
+ " <td>309.0</td>\n",
+ " <td>9141.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>35.0</td>\n",
+ " <td>36.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>35.0</td>\n",
- " <td>8735.0</td>\n",
- " <td>8735.0</td>\n",
- " <td>8735.0</td>\n",
+ " <td>36.0</td>\n",
+ " <td>9450.0</td>\n",
+ " <td>9450.0</td>\n",
+ " <td>9450.0</td>\n",
" <td>2</td>\n",
" <td>0.0</td>\n",
" <td>1.0</td>\n",
- " <td>64.0</td>\n",
- " <td>7.0</td>\n",
- " <td>71.0</td>\n",
+ " <td>706.0</td>\n",
+ " <td>9.0</td>\n",
+ " <td>715.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200416</td>\n",
+ " <td>20200417</td>\n",
" <td>AL</td>\n",
- " <td>4345.0</td>\n",
- " <td>32046.0</td>\n",
+ " <td>4530.0</td>\n",
+ " <td>33318.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>553.0</td>\n",
+ " <td>594.0</td>\n",
" <td>NaN</td>\n",
- " <td>227.0</td>\n",
+ " <td>247.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>553.0</td>\n",
- " <td>36391.0</td>\n",
- " <td>36391.0</td>\n",
- " <td>36391.0</td>\n",
+ " <td>594.0</td>\n",
+ " <td>37848.0</td>\n",
+ " <td>37848.0</td>\n",
+ " <td>37848.0</td>\n",
" <td>1</td>\n",
- " <td>12.0</td>\n",
- " <td>28.0</td>\n",
- " <td>2082.0</td>\n",
- " <td>232.0</td>\n",
- " <td>2314.0</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",
" </tr>\n",
" </tbody>\n",
"</table>\n",
@@ -421,24 +421,24 @@
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200416 AK 300.0 8435.0 NaN NaN \n",
- "1 20200416 AL 4345.0 32046.0 NaN NaN \n",
+ "0 20200417 AK 309.0 9141.0 NaN NaN \n",
+ "1 20200417 AL 4530.0 33318.0 NaN NaN \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
- "0 35.0 NaN NaN \n",
- "1 553.0 NaN 227.0 \n",
+ "0 36.0 NaN NaN \n",
+ "1 594.0 NaN 247.0 \n",
"\n",
" onVentilatorCurrently ... hospitalized total totalTestResults \\\n",
- "0 NaN ... 35.0 8735.0 8735.0 \n",
- "1 NaN ... 553.0 36391.0 36391.0 \n",
+ "0 NaN ... 36.0 9450.0 9450.0 \n",
+ "1 NaN ... 594.0 37848.0 37848.0 \n",
"\n",
" posNeg fips deathIncrease hospitalizedIncrease negativeIncrease \\\n",
- "0 8735.0 2 0.0 1.0 64.0 \n",
- "1 36391.0 1 12.0 28.0 2082.0 \n",
+ "0 9450.0 2 0.0 1.0 706.0 \n",
+ "1 37848.0 1 11.0 41.0 1272.0 \n",
"\n",
" positiveIncrease totalTestResultsIncrease \n",
- "0 7.0 71.0 \n",
- "1 232.0 2314.0 \n",
+ "0 9.0 715.0 \n",
+ "1 185.0 1457.0 \n",
"\n",
"[2 rows x 25 columns]"
]
@@ -474,18 +474,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 6.416916,
- "end_time": "2020-04-17T07:25:17.633251",
+ "duration": 2.571431,
+ "end_time": "2020-04-18T18:11:06.657430",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/pnqb5z0q/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/lvwjkfpt/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/pnqb5z0q/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/lvwjkfpt/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-04-17T07:25:11.216335",
+ "start_time": "2020-04-18T18:11:04.085999",
"version": "1.1.0"
}
},