diff --git a/.renku/workflow/e25674859ffe42549abfa4d7c1dcfc7b.cwl b/.renku/workflow/e25674859ffe42549abfa4d7c1dcfc7b.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..865b8e8feae91b1c7b3d964261dd582d897ea421
--- /dev/null
+++ b/.renku/workflow/e25674859ffe42549abfa4d7c1dcfc7b.cwl
@@ -0,0 +1,120 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: out_folder
+ streamable: false
+ type: string
+ input_2:
+ default: data/covidtracking
+ streamable: false
+ type: string
+ input_3:
+ default:
+ class: File
+ path: ../../notebooks/process/download-covidtracking-data.ipynb
+ streamable: false
+ type: File
+ input_4:
+ default: runs/download-covidtracking-data.runs.ipynb
+ streamable: false
+ type: string
+ input_5:
+ default: states-metadata.json
+ streamable: false
+ type: string
+ input_6:
+ default: states-daily.json
+ streamable: false
+ type: string
+outputs:
+ output_1:
+ outputSource: step_1/output_1
+ streamable: false
+ type: Directory
+ output_3:
+ outputSource: step_1/output_0
+ streamable: false
+ type: File
+requirements: []
+steps:
+ step_1:
+ in:
+ input_1: input_1
+ input_2: input_2
+ input_3: input_3
+ input_4: input_4
+ out:
+ - output_0
+ - output_1
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
+ step_2:
+ in:
+ filename: input_5
+ input_directory: step_1/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_3:
+ in:
+ filename: input_6
+ input_directory: step_1/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 d8bf3a130ebae67ffc01a7952ab7c870aa8ffd59..27dfd82d2a76732f2a0bf6c291926c933d1944c2 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 sha256:2ed9e011d2eee5b892662c6ac60fa8dc40c81e35db6702d0f0caf6a8891530b6
-size 2806544
+oid sha256:b53d5ec861e859d9c4b5d92c824a94cf34fccdc411feee3fe450ca1b3566e6aa
+size 2945856
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index f7c2f3a122f7891344445fdc6eb99876f99b3a28..095f192b9ce6cf9f53c642a5b9c7516e9050cf4e 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 sha256:006c2bec36b15b3b02750aa6b4f65f2b58c03ef27674bbc7bac7bdf547caf00b
-size 34988
+oid sha256:23628a019bf4b14d081e8b8519be4be9ee4712078cae76e8f455f72c066ffb9c
+size 35330
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 5de27e17d3d95b41a503b37e9c903d98a6a5af52..2bbab0ab4fd1eaa30698e8babf1489f14b23ab02 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": 3.237693,
- "end_time": "2020-05-29T07:27:31.480700",
+ "duration": 0.52214,
+ "end_time": "2020-06-02T08:11:09.503843",
"exception": false,
- "start_time": "2020-05-29T07:27:28.243007",
+ "start_time": "2020-06-02T08:11:08.981703",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.019555,
- "end_time": "2020-05-29T07:27:31.511133",
+ "duration": 0.021722,
+ "end_time": "2020-06-02T08:11:09.539612",
"exception": false,
- "start_time": "2020-05-29T07:27:31.491578",
+ "start_time": "2020-06-02T08:11:09.517890",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.019505,
- "end_time": "2020-05-29T07:27:31.542455",
+ "duration": 0.022346,
+ "end_time": "2020-06-02T08:11:09.570298",
"exception": false,
- "start_time": "2020-05-29T07:27:31.522950",
+ "start_time": "2020-06-02T08:11:09.547952",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/8w_tcx45/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/_29it5g5/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": 0.008692,
- "end_time": "2020-05-29T07:27:31.565346",
+ "duration": 0.006388,
+ "end_time": "2020-06-02T08:11:09.585324",
"exception": false,
- "start_time": "2020-05-29T07:27:31.556654",
+ "start_time": "2020-06-02T08:11:09.578936",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.72501,
- "end_time": "2020-05-29T07:27:32.299043",
+ "duration": 0.620735,
+ "end_time": "2020-06-02T08:11:10.212779",
"exception": false,
- "start_time": "2020-05-29T07:27:31.574033",
+ "start_time": "2020-06-02T08:11:09.592044",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.021449,
- "end_time": "2020-05-29T07:27:32.330516",
+ "duration": 0.028753,
+ "end_time": "2020-06-02T08:11:10.257183",
"exception": false,
- "start_time": "2020-05-29T07:27:32.309067",
+ "start_time": "2020-06-02T08:11:10.228430",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.074782,
- "end_time": "2020-05-29T07:27:32.415415",
+ "duration": 0.048608,
+ "end_time": "2020-06-02T08:11:10.315976",
"exception": false,
- "start_time": "2020-05-29T07:27:32.340633",
+ "start_time": "2020-06-02T08:11:10.267368",
"status": "completed"
},
"tags": []
@@ -246,10 +246,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007798,
- "end_time": "2020-05-29T07:27:32.434642",
+ "duration": 0.00642,
+ "end_time": "2020-06-02T08:11:10.329275",
"exception": false,
- "start_time": "2020-05-29T07:27:32.426844",
+ "start_time": "2020-06-02T08:11:10.322855",
"status": "completed"
},
"tags": []
@@ -263,10 +263,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 5.079992,
- "end_time": "2020-05-29T07:27:37.522708",
+ "duration": 5.270376,
+ "end_time": "2020-06-02T08:11:15.606304",
"exception": false,
- "start_time": "2020-05-29T07:27:32.442716",
+ "start_time": "2020-06-02T08:11:10.335928",
"status": "completed"
},
"tags": []
@@ -283,10 +283,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.03146,
- "end_time": "2020-05-29T07:27:37.568666",
+ "duration": 0.033573,
+ "end_time": "2020-06-02T08:11:15.657902",
"exception": false,
- "start_time": "2020-05-29T07:27:37.537206",
+ "start_time": "2020-06-02T08:11:15.624329",
"status": "completed"
},
"tags": []
@@ -305,10 +305,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.1763,
- "end_time": "2020-05-29T07:27:37.756153",
+ "duration": 0.157194,
+ "end_time": "2020-06-02T08:11:15.830240",
"exception": false,
- "start_time": "2020-05-29T07:27:37.579853",
+ "start_time": "2020-06-02T08:11:15.673046",
"status": "completed"
},
"tags": []
@@ -318,7 +318,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "4721 data points\n"
+ "4945 data points\n"
]
},
{
@@ -368,51 +368,51 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200528</td>\n",
+ " <td>20200601</td>\n",
" <td>AK</td>\n",
- " <td>425.0</td>\n",
- " <td>47545.0</td>\n",
+ " <td>467.0</td>\n",
+ " <td>53723.0</td>\n",
" <td>NaN</td>\n",
" <td>10.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>NaN</td>\n",
+ " <td>1.0</td>\n",
" <td>...</td>\n",
" <td>NaN</td>\n",
- " <td>47970</td>\n",
- " <td>47970</td>\n",
- " <td>47970</td>\n",
+ " <td>54190</td>\n",
+ " <td>54190</td>\n",
+ " <td>54190</td>\n",
" <td>2</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
- " <td>1594.0</td>\n",
- " <td>13.0</td>\n",
- " <td>1607.0</td>\n",
+ " <td>2462.0</td>\n",
+ " <td>33.0</td>\n",
+ " <td>2495.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200528</td>\n",
+ " <td>20200601</td>\n",
" <td>AL</td>\n",
- " <td>16310.0</td>\n",
- " <td>184171.0</td>\n",
+ " <td>18363.0</td>\n",
+ " <td>205160.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>1765.0</td>\n",
+ " <td>1856.0</td>\n",
" <td>NaN</td>\n",
- " <td>566.0</td>\n",
+ " <td>591.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>1765.0</td>\n",
- " <td>200481</td>\n",
- " <td>200481</td>\n",
- " <td>200481</td>\n",
+ " <td>1856.0</td>\n",
+ " <td>223523</td>\n",
+ " <td>223523</td>\n",
+ " <td>223523</td>\n",
" <td>1</td>\n",
- " <td>9.0</td>\n",
- " <td>46.0</td>\n",
- " <td>4220.0</td>\n",
- " <td>467.0</td>\n",
- " <td>4687.0</td>\n",
+ " <td>15.0</td>\n",
+ " <td>12.0</td>\n",
+ " <td>5510.0</td>\n",
+ " <td>460.0</td>\n",
+ " <td>5970.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
@@ -421,24 +421,24 @@
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200528 AK 425.0 47545.0 NaN 10.0 \n",
- "1 20200528 AL 16310.0 184171.0 NaN NaN \n",
+ "0 20200601 AK 467.0 53723.0 NaN 10.0 \n",
+ "1 20200601 AL 18363.0 205160.0 NaN NaN \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 1765.0 NaN 566.0 \n",
+ "1 1856.0 NaN 591.0 \n",
"\n",
" onVentilatorCurrently ... hospitalized total totalTestResults posNeg \\\n",
- "0 NaN ... NaN 47970 47970 47970 \n",
- "1 NaN ... 1765.0 200481 200481 200481 \n",
+ "0 1.0 ... NaN 54190 54190 54190 \n",
+ "1 NaN ... 1856.0 223523 223523 223523 \n",
"\n",
" fips deathIncrease hospitalizedIncrease negativeIncrease \\\n",
- "0 2 0.0 0.0 1594.0 \n",
- "1 1 9.0 46.0 4220.0 \n",
+ "0 2 0.0 0.0 2462.0 \n",
+ "1 1 15.0 12.0 5510.0 \n",
"\n",
" positiveIncrease totalTestResultsIncrease \n",
- "0 13.0 1607.0 \n",
- "1 467.0 4687.0 \n",
+ "0 33.0 2495.0 \n",
+ "1 460.0 5970.0 \n",
"\n",
"[2 rows x 27 columns]"
]
@@ -474,18 +474,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 11.277959,
- "end_time": "2020-05-29T07:27:38.075952",
+ "duration": 8.164183,
+ "end_time": "2020-06-02T08:11:16.160309",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/8w_tcx45/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/_29it5g5/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/8w_tcx45/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/_29it5g5/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-05-29T07:27:26.797993",
+ "start_time": "2020-06-02T08:11:07.996126",
"version": "1.1.0"
}
},