diff --git a/.renku/workflow/be48b573811f4258a795df4ae2c84937.cwl b/.renku/workflow/be48b573811f4258a795df4ae2c84937.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..c1d52485f0a8275ece82b8069c705bec920f23b3
--- /dev/null
+++ b/.renku/workflow/be48b573811f4258a795df4ae2c84937.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_0:
+ 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 dcfd7c8fab42dace95badaad423216980b4a0652..de414172519031b93cbaf992183832158654c5a6 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 sha256:85e01cdb4e2eebfca29eaa4b8ee54a1118d83a07fe0aeb850c5a06128cece782
-size 1719955
+oid sha256:70474d63b9aafdc369d2143b9051b0dee786afc00eb29a4bc3a44666975032a7
+size 2005796
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
new file mode 100644
index 0000000000000000000000000000000000000000..bbd2a5489c5504a9b5d7823fa0c800f8059b9fa2
--- /dev/null
+++ b/data/covidtracking/states-metadata.json
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3792fa70653138f0f689985f9444a90e7e3e55c318758a810ad70ee5ec992b94
+size 30347
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index e78530ceb31f2d682b4f1d26e896a8291140661c..5eaafae07e5a58966ccdd9f43270715fd2b4ba91 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": 1.763764,
- "end_time": "2020-05-05T07:26:12.036013",
+ "duration": 3.753366,
+ "end_time": "2020-05-06T16:45:40.992104",
"exception": false,
- "start_time": "2020-05-05T07:26:10.272249",
+ "start_time": "2020-05-06T16:45:37.238738",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.018638,
- "end_time": "2020-05-05T07:26:12.069244",
+ "duration": 0.025891,
+ "end_time": "2020-05-06T16:45:41.033145",
"exception": false,
- "start_time": "2020-05-05T07:26:12.050606",
+ "start_time": "2020-05-06T16:45:41.007254",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.021118,
- "end_time": "2020-05-05T07:26:12.097585",
+ "duration": 0.026262,
+ "end_time": "2020-05-06T16:45:41.075071",
"exception": false,
- "start_time": "2020-05-05T07:26:12.076467",
+ "start_time": "2020-05-06T16:45:41.048809",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/1thbz0bs/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/3ek7e62r/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": 0.007639,
- "end_time": "2020-05-05T07:26:12.113215",
+ "duration": 0.008412,
+ "end_time": "2020-05-06T16:45:41.097518",
"exception": false,
- "start_time": "2020-05-05T07:26:12.105576",
+ "start_time": "2020-05-06T16:45:41.089106",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.596509,
- "end_time": "2020-05-05T07:26:12.715280",
+ "duration": 0.872244,
+ "end_time": "2020-05-06T16:45:41.976828",
"exception": false,
- "start_time": "2020-05-05T07:26:12.118771",
+ "start_time": "2020-05-06T16:45:41.104584",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.028099,
- "end_time": "2020-05-05T07:26:12.759016",
+ "duration": 0.027952,
+ "end_time": "2020-05-06T16:45:42.019412",
"exception": false,
- "start_time": "2020-05-05T07:26:12.730917",
+ "start_time": "2020-05-06T16:45:41.991460",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.093068,
- "end_time": "2020-05-05T07:26:12.862312",
+ "duration": 0.080357,
+ "end_time": "2020-05-06T16:45:42.106205",
"exception": false,
- "start_time": "2020-05-05T07:26:12.769244",
+ "start_time": "2020-05-06T16:45:42.025848",
"status": "completed"
},
"tags": []
@@ -246,10 +246,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007759,
- "end_time": "2020-05-05T07:26:12.885178",
+ "duration": 0.008296,
+ "end_time": "2020-05-06T16:45:42.127234",
"exception": false,
- "start_time": "2020-05-05T07:26:12.877419",
+ "start_time": "2020-05-06T16:45:42.118938",
"status": "completed"
},
"tags": []
@@ -263,10 +263,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.1244,
- "end_time": "2020-05-05T07:26:13.016330",
+ "duration": 0.129224,
+ "end_time": "2020-05-06T16:45:42.262961",
"exception": false,
- "start_time": "2020-05-05T07:26:12.891930",
+ "start_time": "2020-05-06T16:45:42.133737",
"status": "completed"
},
"tags": []
@@ -283,10 +283,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.029959,
- "end_time": "2020-05-05T07:26:13.059745",
+ "duration": 0.036773,
+ "end_time": "2020-05-06T16:45:42.318840",
"exception": false,
- "start_time": "2020-05-05T07:26:13.029786",
+ "start_time": "2020-05-06T16:45:42.282067",
"status": "completed"
},
"tags": []
@@ -305,10 +305,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.124383,
- "end_time": "2020-05-05T07:26:13.194313",
+ "duration": 0.130893,
+ "end_time": "2020-05-06T16:45:42.463122",
"exception": false,
- "start_time": "2020-05-05T07:26:13.069930",
+ "start_time": "2020-05-06T16:45:42.332229",
"status": "completed"
},
"tags": []
@@ -318,7 +318,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "3377 data points\n"
+ "3433 data points\n"
]
},
{
@@ -368,79 +368,79 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200504</td>\n",
+ " <td>20200505</td>\n",
" <td>AK</td>\n",
- " <td>370.0</td>\n",
- " <td>21353.0</td>\n",
+ " <td>371.0</td>\n",
+ " <td>22321.0</td>\n",
" <td>NaN</td>\n",
- " <td>12.0</td>\n",
+ " <td>13.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
" <td>NaN</td>\n",
- " <td>21723.0</td>\n",
- " <td>21723.0</td>\n",
- " <td>21723.0</td>\n",
+ " <td>22692</td>\n",
+ " <td>22692</td>\n",
+ " <td>22692</td>\n",
" <td>2</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
- " <td>143.0</td>\n",
- " <td>2.0</td>\n",
- " <td>145.0</td>\n",
+ " <td>968.0</td>\n",
+ " <td>1.0</td>\n",
+ " <td>969.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200504</td>\n",
+ " <td>20200505</td>\n",
" <td>AL</td>\n",
- " <td>8025.0</td>\n",
- " <td>95092.0</td>\n",
+ " <td>8285.0</td>\n",
+ " <td>98481.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>1064.0</td>\n",
+ " <td>1107.0</td>\n",
" <td>NaN</td>\n",
- " <td>411.0</td>\n",
+ " <td>428.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>1064.0</td>\n",
- " <td>103117.0</td>\n",
- " <td>103117.0</td>\n",
- " <td>103117.0</td>\n",
+ " <td>1107.0</td>\n",
+ " <td>106766</td>\n",
+ " <td>106766</td>\n",
+ " <td>106766</td>\n",
" <td>1</td>\n",
- " <td>6.0</td>\n",
- " <td>29.0</td>\n",
- " <td>10317.0</td>\n",
- " <td>300.0</td>\n",
- " <td>10617.0</td>\n",
+ " <td>17.0</td>\n",
+ " <td>43.0</td>\n",
+ " <td>3389.0</td>\n",
+ " <td>260.0</td>\n",
+ " <td>3649.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
- "<p>2 rows × 25 columns</p>\n",
+ "<p>2 rows × 27 columns</p>\n",
"</div>"
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200504 AK 370.0 21353.0 NaN 12.0 \n",
- "1 20200504 AL 8025.0 95092.0 NaN NaN \n",
+ "0 20200505 AK 371.0 22321.0 NaN 13.0 \n",
+ "1 20200505 AL 8285.0 98481.0 NaN NaN \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 1064.0 NaN 411.0 \n",
+ "1 1107.0 NaN 428.0 \n",
"\n",
- " onVentilatorCurrently ... hospitalized total totalTestResults \\\n",
- "0 NaN ... NaN 21723.0 21723.0 \n",
- "1 NaN ... 1064.0 103117.0 103117.0 \n",
+ " onVentilatorCurrently ... hospitalized total totalTestResults posNeg \\\n",
+ "0 NaN ... NaN 22692 22692 22692 \n",
+ "1 NaN ... 1107.0 106766 106766 106766 \n",
"\n",
- " posNeg fips deathIncrease hospitalizedIncrease negativeIncrease \\\n",
- "0 21723.0 2 0.0 0.0 143.0 \n",
- "1 103117.0 1 6.0 29.0 10317.0 \n",
+ " fips deathIncrease hospitalizedIncrease negativeIncrease \\\n",
+ "0 2 0.0 0.0 968.0 \n",
+ "1 1 17.0 43.0 3389.0 \n",
"\n",
" positiveIncrease totalTestResultsIncrease \n",
- "0 2.0 145.0 \n",
- "1 300.0 10617.0 \n",
+ "0 1.0 969.0 \n",
+ "1 260.0 3649.0 \n",
"\n",
- "[2 rows x 25 columns]"
+ "[2 rows x 27 columns]"
]
},
"execution_count": 9,
@@ -474,18 +474,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 4.468313,
- "end_time": "2020-05-05T07:26:13.523292",
+ "duration": 7.889209,
+ "end_time": "2020-05-06T16:45:42.790180",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/1thbz0bs/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/3ek7e62r/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/1thbz0bs/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/3ek7e62r/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-05-05T07:26:09.054979",
+ "start_time": "2020-05-06T16:45:34.900971",
"version": "1.1.0"
}
},