diff --git a/.renku/workflow/6aa5ea2d03b14d689f578036249fe95d.cwl b/.renku/workflow/6aa5ea2d03b14d689f578036249fe95d.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..0706b4c171457d8aa2cb7321e9e83debe45d2e6a
--- /dev/null
+++ b/.renku/workflow/6aa5ea2d03b14d689f578036249fe95d.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_0
+ streamable: false
+ type: File
+ output_2:
+ outputSource: step_1/output_1
+ streamable: false
+ type: Directory
+requirements: []
+steps:
+ step_1:
+ in:
+ input_1: input_1
+ input_2: input_2
+ input_3: input_3
+ input_4: input_4
+ out:
+ - output_1
+ - output_0
+ 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 2ef7a94b9e6ca9713aac7880935461164f254ea9..f9511b9d543baad447045c301176571457b47bea 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 sha256:67255b1e05d56673f617211475ae7382a424a0bbf8677027f093af68e18371a2
-size 16593726
+oid sha256:d05cadde142e9761e134187a2aae02b5edfe1c25554745fdf29ed624114d3f6b
+size 16674314
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 541e24a427727a768df9d19e38d650a103bf6de2..f60e49bfdb8951a64d7261b84022adfb8f71c4ff 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:a8536ccfa026b52f0635b7f7784528659d34bb649c7926a58f745638fe473603
-size 93245
+oid sha256:20e8b8e025c72bbe1cd5ed0b5fed9d69b92988e69fded0aa3e90e7b5d2b33602
+size 93629
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 318a071dcc576e09c153cde3c77fd32720a04e0f..bf46b35cda103fc0796696e0c4bd8888641f84c7 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": 5.039858,
- "end_time": "2020-10-09T07:35:55.107825",
+ "duration": 4.141087,
+ "end_time": "2020-10-10T07:36:12.587131",
"exception": false,
- "start_time": "2020-10-09T07:35:50.067967",
+ "start_time": "2020-10-10T07:36:08.446044",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.02273,
- "end_time": "2020-10-09T07:35:55.144732",
+ "duration": 0.023581,
+ "end_time": "2020-10-10T07:36:12.625762",
"exception": false,
- "start_time": "2020-10-09T07:35:55.122002",
+ "start_time": "2020-10-10T07:36:12.602181",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.019907,
- "end_time": "2020-10-09T07:35:55.172075",
+ "duration": 0.021272,
+ "end_time": "2020-10-10T07:36:12.657544",
"exception": false,
- "start_time": "2020-10-09T07:35:55.152168",
+ "start_time": "2020-10-10T07:36:12.636272",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/b6rd_660/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/3wa_fl25/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": 0.007406,
- "end_time": "2020-10-09T07:35:55.187217",
+ "duration": 0.006373,
+ "end_time": "2020-10-10T07:36:12.671647",
"exception": false,
- "start_time": "2020-10-09T07:35:55.179811",
+ "start_time": "2020-10-10T07:36:12.665274",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.72549,
- "end_time": "2020-10-09T07:35:55.918437",
+ "duration": 0.609405,
+ "end_time": "2020-10-10T07:36:13.286735",
"exception": false,
- "start_time": "2020-10-09T07:35:55.192947",
+ "start_time": "2020-10-10T07:36:12.677330",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.039673,
- "end_time": "2020-10-09T07:35:55.972214",
+ "duration": 0.025046,
+ "end_time": "2020-10-10T07:36:13.325934",
"exception": false,
- "start_time": "2020-10-09T07:35:55.932541",
+ "start_time": "2020-10-10T07:36:13.300888",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.095726,
- "end_time": "2020-10-09T07:35:56.082363",
+ "duration": 0.079111,
+ "end_time": "2020-10-10T07:36:13.413252",
"exception": false,
- "start_time": "2020-10-09T07:35:55.986637",
+ "start_time": "2020-10-10T07:36:13.334141",
"status": "completed"
},
"tags": []
@@ -280,10 +280,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007992,
- "end_time": "2020-10-09T07:35:56.102328",
+ "duration": 0.008056,
+ "end_time": "2020-10-10T07:36:13.433828",
"exception": false,
- "start_time": "2020-10-09T07:35:56.094336",
+ "start_time": "2020-10-10T07:36:13.425772",
"status": "completed"
},
"tags": []
@@ -297,10 +297,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 27.608821,
- "end_time": "2020-10-09T07:36:23.717683",
+ "duration": 29.130323,
+ "end_time": "2020-10-10T07:36:42.570502",
"exception": false,
- "start_time": "2020-10-09T07:35:56.108862",
+ "start_time": "2020-10-10T07:36:13.440179",
"status": "completed"
},
"tags": []
@@ -317,10 +317,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.050585,
- "end_time": "2020-10-09T07:36:23.786610",
+ "duration": 0.052462,
+ "end_time": "2020-10-10T07:36:42.649433",
"exception": false,
- "start_time": "2020-10-09T07:36:23.736025",
+ "start_time": "2020-10-10T07:36:42.596971",
"status": "completed"
},
"tags": []
@@ -339,10 +339,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.530285,
- "end_time": "2020-10-09T07:36:24.331862",
+ "duration": 0.54206,
+ "end_time": "2020-10-10T07:36:43.205917",
"exception": false,
- "start_time": "2020-10-09T07:36:23.801577",
+ "start_time": "2020-10-10T07:36:42.663857",
"status": "completed"
},
"tags": []
@@ -352,7 +352,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "12250 data points\n"
+ "12309 data points\n"
]
},
{
@@ -402,21 +402,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201008</td>\n",
+ " <td>20201009</td>\n",
" <td>AK</td>\n",
- " <td>9996.0</td>\n",
+ " <td>10176.0</td>\n",
" <td>NaN</td>\n",
- " <td>481175.0</td>\n",
+ " <td>482894.0</td>\n",
" <td>NaN</td>\n",
- " <td>491171.0</td>\n",
- " <td>46.0</td>\n",
+ " <td>493070.0</td>\n",
+ " <td>51.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>491171</td>\n",
- " <td>1</td>\n",
+ " <td>493070</td>\n",
+ " <td>0</td>\n",
" <td>0</td>\n",
- " <td>7232d5fe7f4dd05983c93f2954527e68736578c6</td>\n",
+ " <td>3c160d82e90df263b41bbb98bcc4d2f6d17ff9eb</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -426,21 +426,21 @@
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20201008</td>\n",
+ " <td>20201009</td>\n",
" <td>AL</td>\n",
- " <td>161975.0</td>\n",
- " <td>19311.0</td>\n",
- " <td>1042046.0</td>\n",
+ " <td>163465.0</td>\n",
+ " <td>19565.0</td>\n",
+ " <td>1052552.0</td>\n",
" <td>NaN</td>\n",
- " <td>1184710.0</td>\n",
- " <td>754.0</td>\n",
+ " <td>1196452.0</td>\n",
+ " <td>816.0</td>\n",
" <td>17989.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>1204021</td>\n",
- " <td>36</td>\n",
- " <td>74</td>\n",
- " <td>6ffc9058ab0b1b61e62ff3a69eb2964a1b867624</td>\n",
+ " <td>1216017</td>\n",
+ " <td>16</td>\n",
+ " <td>0</td>\n",
+ " <td>d4b09eb0f40a7865f284fcbc22f19ca0f68b4f12</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -455,20 +455,20 @@
],
"text/plain": [
" date state positive probableCases negative pending \\\n",
- "0 20201008 AK 9996.0 NaN 481175.0 NaN \n",
- "1 20201008 AL 161975.0 19311.0 1042046.0 NaN \n",
+ "0 20201009 AK 10176.0 NaN 482894.0 NaN \n",
+ "1 20201009 AL 163465.0 19565.0 1052552.0 NaN \n",
"\n",
" totalTestResults hospitalizedCurrently hospitalizedCumulative \\\n",
- "0 491171.0 46.0 NaN \n",
- "1 1184710.0 754.0 17989.0 \n",
+ "0 493070.0 51.0 NaN \n",
+ "1 1196452.0 816.0 17989.0 \n",
"\n",
" inIcuCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 NaN ... 491171 1 0 \n",
- "1 NaN ... 1204021 36 74 \n",
+ "0 NaN ... 493070 0 0 \n",
+ "1 NaN ... 1216017 16 0 \n",
"\n",
" hash commercialScore \\\n",
- "0 7232d5fe7f4dd05983c93f2954527e68736578c6 0 \n",
- "1 6ffc9058ab0b1b61e62ff3a69eb2964a1b867624 0 \n",
+ "0 3c160d82e90df263b41bbb98bcc4d2f6d17ff9eb 0 \n",
+ "1 d4b09eb0f40a7865f284fcbc22f19ca0f68b4f12 0 \n",
"\n",
" negativeRegularScore negativeScore positiveScore score grade \n",
"0 0 0 0 0 \n",
@@ -508,18 +508,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 36.30637,
- "end_time": "2020-10-09T07:36:24.759090",
+ "duration": 36.952942,
+ "end_time": "2020-10-10T07:36:43.533362",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/b6rd_660/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/3wa_fl25/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/b6rd_660/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/3wa_fl25/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-10-09T07:35:48.452720",
+ "start_time": "2020-10-10T07:36:06.580420",
"version": "1.1.0"
}
},