diff --git a/.renku/workflow/975bb67340ec472c964083369b804c54.cwl b/.renku/workflow/975bb67340ec472c964083369b804c54.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..9e05bcc7dee93e4b72bf898cff064da4fd2175eb
--- /dev/null
+++ b/.renku/workflow/975bb67340ec472c964083369b804c54.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_2:
+ outputSource: step_3/output_0
+ streamable: false
+ type: File
+ output_3:
+ 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_1
+ - output_0
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index ed95224bec56527a5ce3fcbaefcae5aed95c6741..b44e8722f81b43a041abde8addddd63603f60a87 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 sha256:136defefdadf4133e1d20028db3d077e4ea2d141eee730b645374fe90e0e94d7
-size 18613184
+oid sha256:d13d414f947d832478298e57ee307398da1d358358bbbf245fb3f8ae3e767a34
+size 18767338
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index ab83d8c6df6d027658d625adcd14930894114872..4f88595696ce40a1934aff44b43afb016af493b1 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:f4ec8171dd99613eb1b81ecffa35355fe64aa13a460cc8b1a0dd3949e8933a1d
-size 108213
+oid sha256:103a073640921a96c38ee84da94984a61e0bd11362acc39365a39cb70e828533
+size 109181
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index f8622d4e8e9d6d4f631b7b2535bfc7d25f4bb915..f4cc100edb928fe70a5f08b6b4698810a0c6ad74 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": 4.38731,
- "end_time": "2020-11-02T07:40:01.538008",
+ "duration": 4.61991,
+ "end_time": "2020-11-04T07:36:05.231196",
"exception": false,
- "start_time": "2020-11-02T07:39:57.150698",
+ "start_time": "2020-11-04T07:36:00.611286",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.024656,
- "end_time": "2020-11-02T07:40:01.578884",
+ "duration": 0.019678,
+ "end_time": "2020-11-04T07:36:05.263484",
"exception": false,
- "start_time": "2020-11-02T07:40:01.554228",
+ "start_time": "2020-11-04T07:36:05.243806",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.027968,
- "end_time": "2020-11-02T07:40:01.620053",
+ "duration": 0.024073,
+ "end_time": "2020-11-04T07:36:05.295125",
"exception": false,
- "start_time": "2020-11-02T07:40:01.592085",
+ "start_time": "2020-11-04T07:36:05.271052",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/qj7q4luy/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/po7g_8x1/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": 0.008125,
- "end_time": "2020-11-02T07:40:01.638870",
+ "duration": 0.008208,
+ "end_time": "2020-11-04T07:36:05.316133",
"exception": false,
- "start_time": "2020-11-02T07:40:01.630745",
+ "start_time": "2020-11-04T07:36:05.307925",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 1.010529,
- "end_time": "2020-11-02T07:40:02.656587",
+ "duration": 0.691276,
+ "end_time": "2020-11-04T07:36:06.013731",
"exception": false,
- "start_time": "2020-11-02T07:40:01.646058",
+ "start_time": "2020-11-04T07:36:05.322455",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.025484,
- "end_time": "2020-11-02T07:40:02.696195",
+ "duration": 0.025723,
+ "end_time": "2020-11-04T07:36:06.052061",
"exception": false,
- "start_time": "2020-11-02T07:40:02.670711",
+ "start_time": "2020-11-04T07:36:06.026338",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.081021,
- "end_time": "2020-11-02T07:40:02.785478",
+ "duration": 0.073928,
+ "end_time": "2020-11-04T07:36:06.137689",
"exception": false,
- "start_time": "2020-11-02T07:40:02.704457",
+ "start_time": "2020-11-04T07:36:06.063761",
"status": "completed"
},
"tags": []
@@ -280,10 +280,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008282,
- "end_time": "2020-11-02T07:40:02.808385",
+ "duration": 0.009376,
+ "end_time": "2020-11-04T07:36:06.158189",
"exception": false,
- "start_time": "2020-11-02T07:40:02.800103",
+ "start_time": "2020-11-04T07:36:06.148813",
"status": "completed"
},
"tags": []
@@ -297,10 +297,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.486308,
- "end_time": "2020-11-02T07:40:03.301771",
+ "duration": 0.461672,
+ "end_time": "2020-11-04T07:36:06.627415",
"exception": false,
- "start_time": "2020-11-02T07:40:02.815463",
+ "start_time": "2020-11-04T07:36:06.165743",
"status": "completed"
},
"tags": []
@@ -317,10 +317,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.06364,
- "end_time": "2020-11-02T07:40:03.382133",
+ "duration": 0.048019,
+ "end_time": "2020-11-04T07:36:06.690160",
"exception": false,
- "start_time": "2020-11-02T07:40:03.318493",
+ "start_time": "2020-11-04T07:36:06.642141",
"status": "completed"
},
"tags": []
@@ -339,10 +339,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.707388,
- "end_time": "2020-11-02T07:40:04.104186",
+ "duration": 0.5286,
+ "end_time": "2020-11-04T07:36:07.232531",
"exception": false,
- "start_time": "2020-11-02T07:40:03.396798",
+ "start_time": "2020-11-04T07:36:06.703931",
"status": "completed"
},
"tags": []
@@ -352,7 +352,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "13663 data points\n"
+ "13775 data points\n"
]
},
{
@@ -402,21 +402,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201101</td>\n",
+ " <td>20201103</td>\n",
" <td>AK</td>\n",
- " <td>16705.0</td>\n",
+ " <td>17448.0</td>\n",
" <td>NaN</td>\n",
- " <td>587852.0</td>\n",
+ " <td>607307.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>604207.0</td>\n",
- " <td>98.0</td>\n",
+ " <td>624755.0</td>\n",
+ " <td>97.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>604557</td>\n",
- " <td>1</td>\n",
+ " <td>624755</td>\n",
+ " <td>0</td>\n",
" <td>0</td>\n",
- " <td>0fe81cb4b3a17588cfde8bbd309c3f0f2e786fd2</td>\n",
+ " <td>e4b7b20d6a7724e14ce53e37e1d543c6bf1176c9</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>20201101</td>\n",
+ " <td>20201103</td>\n",
" <td>AL</td>\n",
- " <td>193985.0</td>\n",
- " <td>28746.0</td>\n",
- " <td>1187341.0</td>\n",
+ " <td>195929.0</td>\n",
+ " <td>29302.0</td>\n",
+ " <td>1196422.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1352580.0</td>\n",
- " <td>967.0</td>\n",
- " <td>20450.0</td>\n",
+ " <td>1363049.0</td>\n",
+ " <td>1022.0</td>\n",
+ " <td>20901.0</td>\n",
" <td>...</td>\n",
- " <td>1381326</td>\n",
- " <td>6</td>\n",
- " <td>0</td>\n",
- " <td>0bd0f2572848cf6f46a651c076d32afceb8dc6a1</td>\n",
+ " <td>1392351</td>\n",
+ " <td>14</td>\n",
+ " <td>451</td>\n",
+ " <td>f6dd94c1b534c3e4a74e78d1859fcc12ae1ef103</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 20201101 AK 16705.0 NaN 587852.0 NaN \n",
- "1 20201101 AL 193985.0 28746.0 1187341.0 NaN \n",
+ "0 20201103 AK 17448.0 NaN 607307.0 NaN \n",
+ "1 20201103 AL 195929.0 29302.0 1196422.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 604207.0 98.0 \n",
- "1 totalTestsViral 1352580.0 967.0 \n",
+ "0 totalTestsViral 624755.0 97.0 \n",
+ "1 totalTestsViral 1363049.0 1022.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 NaN ... 604557 1 0 \n",
- "1 20450.0 ... 1381326 6 0 \n",
+ "0 NaN ... 624755 0 0 \n",
+ "1 20901.0 ... 1392351 14 451 \n",
"\n",
" hash commercialScore \\\n",
- "0 0fe81cb4b3a17588cfde8bbd309c3f0f2e786fd2 0 \n",
- "1 0bd0f2572848cf6f46a651c076d32afceb8dc6a1 0 \n",
+ "0 e4b7b20d6a7724e14ce53e37e1d543c6bf1176c9 0 \n",
+ "1 f6dd94c1b534c3e4a74e78d1859fcc12ae1ef103 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": 9.174658,
- "end_time": "2020-11-02T07:40:04.530883",
+ "duration": 8.604898,
+ "end_time": "2020-11-04T07:36:07.556382",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/qj7q4luy/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/po7g_8x1/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/qj7q4luy/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/po7g_8x1/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-11-02T07:39:55.356225",
+ "start_time": "2020-11-04T07:35:58.951484",
"version": "1.1.0"
}
},