diff --git a/.renku/workflow/f2dbb09e70314ed4b235c8bf9cdd94a1.cwl b/.renku/workflow/f2dbb09e70314ed4b235c8bf9cdd94a1.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..44b232a29518b43908e2d30f2a9f0b608e260ba1
--- /dev/null
+++ b/.renku/workflow/f2dbb09e70314ed4b235c8bf9cdd94a1.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: 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-metadata.json
+ streamable: false
+ type: string
+outputs:
+ output_0:
+ outputSource: step_2/output_0
+ streamable: false
+ type: File
+ output_1:
+ outputSource: step_2/output_1
+ streamable: false
+ type: Directory
+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-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:
+ input_1: input_2
+ input_2: input_3
+ input_3: input_4
+ input_4: input_5
+ out:
+ - output_1
+ - output_0
+ run: ff5f474d38144c5d882c0036bd1059c2_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-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 3b8367f5b9aca6f2044c5a5ac677a2d5e176abea..a6234d1e50b88259af3c1cf2b985c31f29b74f22 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:cf9f11314c54abdddbb58fc07a2df986bb85d68437223dbe1052203c2505a9ca
-size 142982
+oid sha256:04a4bbec05fc52248512469d41ee013fdce83b6fef928e9562dfe801ad82aff9
+size 151715
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index d0bee96e2baf67ae73b9f2103ca757df8509fd1f..55645103119e9298e27d5465aebaac61a453d438 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:e66567f0258fc7582c4a18e8a1aef3a27182f902aa94121222468c8504ec830f
-size 25452
+oid sha256:7eaff61b1c975bf893a6e7e35a694980140435ce8cb5afc02164ce685cfa5baa
+size 25218
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 158c4445193789ec1ef307b85c72ca0f68c5399f..24fe640f5e06eaf3a6958be870a9f8836ce9564e 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": 2.276469,
- "end_time": "2020-03-23T08:22:22.453561",
+ "duration": 1.484962,
+ "end_time": "2020-03-24T11:08:51.882283",
"exception": false,
- "start_time": "2020-03-23T08:22:20.177092",
+ "start_time": "2020-03-24T11:08:50.397321",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.020852,
- "end_time": "2020-03-23T08:22:22.488968",
+ "duration": 0.034224,
+ "end_time": "2020-03-24T11:08:51.927200",
"exception": false,
- "start_time": "2020-03-23T08:22:22.468116",
+ "start_time": "2020-03-24T11:08:51.892976",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.02465,
- "end_time": "2020-03-23T08:22:22.522182",
+ "duration": 0.024298,
+ "end_time": "2020-03-24T11:08:51.965529",
"exception": false,
- "start_time": "2020-03-23T08:22:22.497532",
+ "start_time": "2020-03-24T11:08:51.941231",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/iocfjzox/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/kq4860jy/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": 0.005919,
- "end_time": "2020-03-23T08:22:22.536991",
+ "duration": 0.007354,
+ "end_time": "2020-03-24T11:08:51.981277",
"exception": false,
- "start_time": "2020-03-23T08:22:22.531072",
+ "start_time": "2020-03-24T11:08:51.973923",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.683247,
- "end_time": "2020-03-23T08:22:23.226480",
+ "duration": 1.994092,
+ "end_time": "2020-03-24T11:08:53.981279",
"exception": false,
- "start_time": "2020-03-23T08:22:22.543233",
+ "start_time": "2020-03-24T11:08:51.987187",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.02999,
- "end_time": "2020-03-23T08:22:23.270771",
+ "duration": 0.028446,
+ "end_time": "2020-03-24T11:08:54.020108",
"exception": false,
- "start_time": "2020-03-23T08:22:23.240781",
+ "start_time": "2020-03-24T11:08:53.991662",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.075074,
- "end_time": "2020-03-23T08:22:23.356315",
+ "duration": 0.080991,
+ "end_time": "2020-03-24T11:08:54.110615",
"exception": false,
- "start_time": "2020-03-23T08:22:23.281241",
+ "start_time": "2020-03-24T11:08:54.029624",
"status": "completed"
},
"tags": []
@@ -187,7 +187,7 @@
" <td>@Alaska_DHSS</td>\n",
" <td>All data</td>\n",
" <td>False</td>\n",
- " <td>Unclear if their reported number means \"person...</td>\n",
+ " <td>We count the reported number as \"persons teste...</td>\n",
" <td>Alaska</td>\n",
" </tr>\n",
" <tr>\n",
@@ -220,7 +220,7 @@
"1 None @alpublichealth \n",
"\n",
" pui pum notes name \n",
- "0 All data False Unclear if their reported number means \"person... Alaska \n",
+ "0 All data False We count the reported number as \"persons teste... Alaska \n",
"1 No data False Last negative count from 3/16. Last update tim... Alabama "
]
},
@@ -239,10 +239,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008205,
- "end_time": "2020-03-23T08:22:23.377337",
+ "duration": 0.010469,
+ "end_time": "2020-03-24T11:08:54.132051",
"exception": false,
- "start_time": "2020-03-23T08:22:23.369132",
+ "start_time": "2020-03-24T11:08:54.121582",
"status": "completed"
},
"tags": []
@@ -256,10 +256,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.216238,
- "end_time": "2020-03-23T08:22:23.599867",
+ "duration": 0.162493,
+ "end_time": "2020-03-24T11:08:54.304650",
"exception": false,
- "start_time": "2020-03-23T08:22:23.383629",
+ "start_time": "2020-03-24T11:08:54.142157",
"status": "completed"
},
"tags": []
@@ -276,10 +276,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.030954,
- "end_time": "2020-03-23T08:22:23.651293",
+ "duration": 0.02792,
+ "end_time": "2020-03-24T11:08:54.344357",
"exception": false,
- "start_time": "2020-03-23T08:22:23.620339",
+ "start_time": "2020-03-24T11:08:54.316437",
"status": "completed"
},
"tags": []
@@ -298,10 +298,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.066839,
- "end_time": "2020-03-23T08:22:23.732970",
+ "duration": 0.06445,
+ "end_time": "2020-03-24T11:08:54.419822",
"exception": false,
- "start_time": "2020-03-23T08:22:23.666131",
+ "start_time": "2020-03-24T11:08:54.355372",
"status": "completed"
},
"tags": []
@@ -311,7 +311,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "925 data points\n"
+ "981 data points\n"
]
},
{
@@ -349,7 +349,7 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200322</td>\n",
+ " <td>20200323</td>\n",
" <td>AK</td>\n",
" <td>22.0</td>\n",
" <td>946.0</td>\n",
@@ -357,19 +357,19 @@
" <td>0.0</td>\n",
" <td>NaN</td>\n",
" <td>968</td>\n",
- " <td>2020-03-22T20:00:00Z</td>\n",
+ " <td>2020-03-23T20:00:00Z</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200322</td>\n",
+ " <td>20200323</td>\n",
" <td>AL</td>\n",
- " <td>138.0</td>\n",
- " <td>1464.0</td>\n",
+ " <td>167.0</td>\n",
+ " <td>1665.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>0.0</td>\n",
- " <td>1602</td>\n",
- " <td>2020-03-22T20:00:00Z</td>\n",
+ " <td>1832</td>\n",
+ " <td>2020-03-23T20:00:00Z</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
@@ -377,12 +377,12 @@
],
"text/plain": [
" date state positive negative pending hospitalized death total \\\n",
- "0 20200322 AK 22.0 946.0 NaN 0.0 NaN 968 \n",
- "1 20200322 AL 138.0 1464.0 NaN NaN 0.0 1602 \n",
+ "0 20200323 AK 22.0 946.0 NaN 0.0 NaN 968 \n",
+ "1 20200323 AL 167.0 1665.0 NaN NaN 0.0 1832 \n",
"\n",
" dateChecked \n",
- "0 2020-03-22T20:00:00Z \n",
- "1 2020-03-22T20:00:00Z "
+ "0 2020-03-23T20:00:00Z \n",
+ "1 2020-03-23T20:00:00Z "
]
},
"execution_count": 9,
@@ -416,18 +416,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 4.883343,
- "end_time": "2020-03-23T08:22:24.072161",
+ "duration": 5.713541,
+ "end_time": "2020-03-24T11:08:54.762805",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/iocfjzox/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/kq4860jy/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/iocfjzox/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/kq4860jy/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-03-23T08:22:19.188818",
+ "start_time": "2020-03-24T11:08:49.049264",
"version": "1.1.0"
}
},