diff --git a/.renku/workflow/c77734ebae3c46bcadc6b53a6eb5286c.cwl b/.renku/workflow/c77734ebae3c46bcadc6b53a6eb5286c.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..48589879bcac5b24368e1a3d40250e7d9a039e73
--- /dev/null
+++ b/.renku/workflow/c77734ebae3c46bcadc6b53a6eb5286c.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_0:
+ outputSource: step_3/output_1
+ streamable: false
+ type: Directory
+ output_1:
+ outputSource: step_3/output_0
+ streamable: false
+ type: File
+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_0
+ - output_1
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index 7ecda5208e31b672b45929bce69e45505b953c3b..a06ba913e983e40c3864760723f51607ecb44b13 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 sha256:3f6acacbc371f762e084fd9d48c2e9737a72b1ffd5fef4123ce595aacd2068d6
-size 1078477
+oid sha256:54d82c1f244f0c66878d1374b1697fac778b9974e13ea78f9f9a4fd098bdc17d
+size 1109673
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index e15c0084ce5c906c55a759b45fd323ea3cb7af4c..0dfcfbcf04fd813eab1ed2b998c64cb2dc0bd391 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 sha256:8f28e386e08c74c818f7d4202080468c77d192b4277025324e85b38b60f42396
-size 27670
+oid sha256:624512e2ac298106608d022e9db30c1e463045310bfe289f7ed0347d21761ea1
+size 28017
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index ad24299b9c0bcc36963f8596440a22826232d66d..de317c9b788315c2989d366db35daaaadfe6a344 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": 3.370891,
- "end_time": "2020-04-15T09:29:48.938163",
+ "duration": 4.850931,
+ "end_time": "2020-04-16T07:25:50.648244",
"exception": false,
- "start_time": "2020-04-15T09:29:45.567272",
+ "start_time": "2020-04-16T07:25:45.797313",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.025216,
- "end_time": "2020-04-15T09:29:48.977787",
+ "duration": 0.023441,
+ "end_time": "2020-04-16T07:25:50.686536",
"exception": false,
- "start_time": "2020-04-15T09:29:48.952571",
+ "start_time": "2020-04-16T07:25:50.663095",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.018894,
- "end_time": "2020-04-15T09:29:49.005279",
+ "duration": 0.019484,
+ "end_time": "2020-04-16T07:25:50.714489",
"exception": false,
- "start_time": "2020-04-15T09:29:48.986385",
+ "start_time": "2020-04-16T07:25:50.695005",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/a08m4hk2/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/0f1d1bh8/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": 0.006272,
- "end_time": "2020-04-15T09:29:49.019358",
+ "duration": 0.005952,
+ "end_time": "2020-04-16T07:25:50.727458",
"exception": false,
- "start_time": "2020-04-15T09:29:49.013086",
+ "start_time": "2020-04-16T07:25:50.721506",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.189619,
- "end_time": "2020-04-15T09:29:49.214833",
+ "duration": 0.280782,
+ "end_time": "2020-04-16T07:25:51.013940",
"exception": false,
- "start_time": "2020-04-15T09:29:49.025214",
+ "start_time": "2020-04-16T07:25:50.733158",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.025798,
- "end_time": "2020-04-15T09:29:49.259176",
+ "duration": 0.024615,
+ "end_time": "2020-04-16T07:25:51.052542",
"exception": false,
- "start_time": "2020-04-15T09:29:49.233378",
+ "start_time": "2020-04-16T07:25:51.027927",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.101309,
- "end_time": "2020-04-15T09:29:49.368407",
+ "duration": 0.08431,
+ "end_time": "2020-04-16T07:25:51.144413",
"exception": false,
- "start_time": "2020-04-15T09:29:49.267098",
+ "start_time": "2020-04-16T07:25:51.060103",
"status": "completed"
},
"tags": []
@@ -246,10 +246,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007654,
- "end_time": "2020-04-15T09:29:49.387684",
+ "duration": 0.007502,
+ "end_time": "2020-04-16T07:25:51.166315",
"exception": false,
- "start_time": "2020-04-15T09:29:49.380030",
+ "start_time": "2020-04-16T07:25:51.158813",
"status": "completed"
},
"tags": []
@@ -263,10 +263,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.390614,
- "end_time": "2020-04-15T09:29:49.784808",
+ "duration": 0.347787,
+ "end_time": "2020-04-16T07:25:51.520681",
"exception": false,
- "start_time": "2020-04-15T09:29:49.394194",
+ "start_time": "2020-04-16T07:25:51.172894",
"status": "completed"
},
"tags": []
@@ -283,10 +283,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.030431,
- "end_time": "2020-04-15T09:29:49.830306",
+ "duration": 0.033695,
+ "end_time": "2020-04-16T07:25:51.571002",
"exception": false,
- "start_time": "2020-04-15T09:29:49.799875",
+ "start_time": "2020-04-16T07:25:51.537307",
"status": "completed"
},
"tags": []
@@ -305,10 +305,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.11653,
- "end_time": "2020-04-15T09:29:49.958509",
+ "duration": 0.102035,
+ "end_time": "2020-04-16T07:25:51.684796",
"exception": false,
- "start_time": "2020-04-15T09:29:49.841979",
+ "start_time": "2020-04-16T07:25:51.582761",
"status": "completed"
},
"tags": []
@@ -318,7 +318,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "2228 data points\n"
+ "2284 data points\n"
]
},
{
@@ -368,51 +368,51 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200414</td>\n",
+ " <td>20200415</td>\n",
" <td>AK</td>\n",
- " <td>285.0</td>\n",
- " <td>8063.0</td>\n",
+ " <td>293.0</td>\n",
+ " <td>8371.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>32.0</td>\n",
+ " <td>34.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>32.0</td>\n",
- " <td>8348.0</td>\n",
- " <td>8348.0</td>\n",
- " <td>8348.0</td>\n",
+ " <td>34.0</td>\n",
+ " <td>8664.0</td>\n",
+ " <td>8664.0</td>\n",
+ " <td>8664.0</td>\n",
" <td>2</td>\n",
- " <td>1.0</td>\n",
" <td>0.0</td>\n",
- " <td>510.0</td>\n",
+ " <td>2.0</td>\n",
+ " <td>308.0</td>\n",
" <td>8.0</td>\n",
- " <td>518.0</td>\n",
+ " <td>316.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200414</td>\n",
+ " <td>20200415</td>\n",
" <td>AL</td>\n",
- " <td>3876.0</td>\n",
- " <td>29241.0</td>\n",
+ " <td>4113.0</td>\n",
+ " <td>29964.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>493.0</td>\n",
+ " <td>525.0</td>\n",
" <td>NaN</td>\n",
- " <td>210.0</td>\n",
+ " <td>219.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>493.0</td>\n",
- " <td>33117.0</td>\n",
- " <td>33117.0</td>\n",
- " <td>33117.0</td>\n",
+ " <td>525.0</td>\n",
+ " <td>34077.0</td>\n",
+ " <td>34077.0</td>\n",
+ " <td>34077.0</td>\n",
" <td>1</td>\n",
" <td>11.0</td>\n",
- " <td>36.0</td>\n",
- " <td>3793.0</td>\n",
- " <td>142.0</td>\n",
- " <td>3935.0</td>\n",
+ " <td>32.0</td>\n",
+ " <td>723.0</td>\n",
+ " <td>237.0</td>\n",
+ " <td>960.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
@@ -421,24 +421,24 @@
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200414 AK 285.0 8063.0 NaN NaN \n",
- "1 20200414 AL 3876.0 29241.0 NaN NaN \n",
+ "0 20200415 AK 293.0 8371.0 NaN NaN \n",
+ "1 20200415 AL 4113.0 29964.0 NaN NaN \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
- "0 32.0 NaN NaN \n",
- "1 493.0 NaN 210.0 \n",
+ "0 34.0 NaN NaN \n",
+ "1 525.0 NaN 219.0 \n",
"\n",
" onVentilatorCurrently ... hospitalized total totalTestResults \\\n",
- "0 NaN ... 32.0 8348.0 8348.0 \n",
- "1 NaN ... 493.0 33117.0 33117.0 \n",
+ "0 NaN ... 34.0 8664.0 8664.0 \n",
+ "1 NaN ... 525.0 34077.0 34077.0 \n",
"\n",
" posNeg fips deathIncrease hospitalizedIncrease negativeIncrease \\\n",
- "0 8348.0 2 1.0 0.0 510.0 \n",
- "1 33117.0 1 11.0 36.0 3793.0 \n",
+ "0 8664.0 2 0.0 2.0 308.0 \n",
+ "1 34077.0 1 11.0 32.0 723.0 \n",
"\n",
" positiveIncrease totalTestResultsIncrease \n",
- "0 8.0 518.0 \n",
- "1 142.0 3935.0 \n",
+ "0 8.0 316.0 \n",
+ "1 237.0 960.0 \n",
"\n",
"[2 rows x 25 columns]"
]
@@ -474,18 +474,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 6.730918,
- "end_time": "2020-04-15T09:29:50.387368",
+ "duration": 8.922259,
+ "end_time": "2020-04-16T07:25:52.005239",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/a08m4hk2/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/0f1d1bh8/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/a08m4hk2/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/0f1d1bh8/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-04-15T09:29:43.656450",
+ "start_time": "2020-04-16T07:25:43.082980",
"version": "1.1.0"
}
},