diff --git a/.renku/workflow/4ca72939ee54419881b0c889cb2cf1c8.cwl b/.renku/workflow/4ca72939ee54419881b0c889cb2cf1c8.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..0394e19d1ecadcc35e1545f7475e29ea6ec7fbcc
--- /dev/null
+++ b/.renku/workflow/4ca72939ee54419881b0c889cb2cf1c8.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_1:
+ outputSource: step_2/output_1
+ streamable: false
+ type: Directory
+ output_3:
+ outputSource: step_2/output_0
+ streamable: false
+ type: File
+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_0
+ - output_1
+ run: a17d560c41a54f5aa307ce5f3c5effe5_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 938d781a19defccd5281e8b4fd9106a61eafd6bf..99d721ed2bb48353d1b37776794212205bd6dc5d 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:aa3df90aa736945958fbe2cd80fcd082f035331d499dcbd75b64af1dff5fd2e1
-size 15735063
+oid sha256:df4a48da05c6878a61511c2021a5d411742ae4073d16763f803115cf8900784d
+size 15810522
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
new file mode 100644
index 0000000000000000000000000000000000000000..77e163455bff354a0cb4b4fb0b377271170fabfa
--- /dev/null
+++ b/data/covidtracking/states-metadata.json
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2868a9d42f7c9acf305bbb3fb7b2cb1bc8da99abdeb0414c9ab0bfaf1d7e03c3
+size 88112
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 54ace4414bd97b0ec7c6a2f0ee6ace80aaf542b0..1961076cc5bb56c6465cb1040dfc1a8bff986b3f 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": 5.487441,
- "end_time": "2020-10-01T07:35:42.748342",
+ "duration": 4.046085,
+ "end_time": "2020-10-02T07:38:06.758857",
"exception": false,
- "start_time": "2020-10-01T07:35:37.260901",
+ "start_time": "2020-10-02T07:38:02.712772",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.025453,
- "end_time": "2020-10-01T07:35:42.791837",
+ "duration": 0.025391,
+ "end_time": "2020-10-02T07:38:06.803555",
"exception": false,
- "start_time": "2020-10-01T07:35:42.766384",
+ "start_time": "2020-10-02T07:38:06.778164",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.0231,
- "end_time": "2020-10-01T07:35:42.826930",
+ "duration": 0.02627,
+ "end_time": "2020-10-02T07:38:06.839437",
"exception": false,
- "start_time": "2020-10-01T07:35:42.803830",
+ "start_time": "2020-10-02T07:38:06.813167",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/85owm2w1/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/el6ip4bh/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": 0.006447,
- "end_time": "2020-10-01T07:35:42.841265",
+ "duration": 0.008354,
+ "end_time": "2020-10-02T07:38:06.861958",
"exception": false,
- "start_time": "2020-10-01T07:35:42.834818",
+ "start_time": "2020-10-02T07:38:06.853604",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.707094,
- "end_time": "2020-10-01T07:35:43.554367",
+ "duration": 0.758127,
+ "end_time": "2020-10-02T07:38:07.627135",
"exception": false,
- "start_time": "2020-10-01T07:35:42.847273",
+ "start_time": "2020-10-02T07:38:06.869008",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.027626,
- "end_time": "2020-10-01T07:35:43.595490",
+ "duration": 0.02875,
+ "end_time": "2020-10-02T07:38:07.669426",
"exception": false,
- "start_time": "2020-10-01T07:35:43.567864",
+ "start_time": "2020-10-02T07:38:07.640676",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.086305,
- "end_time": "2020-10-01T07:35:43.690577",
+ "duration": 0.109723,
+ "end_time": "2020-10-02T07:38:07.793523",
"exception": false,
- "start_time": "2020-10-01T07:35:43.604272",
+ "start_time": "2020-10-02T07:38:07.683800",
"status": "completed"
},
"tags": []
@@ -280,10 +280,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.00807,
- "end_time": "2020-10-01T07:35:43.711186",
+ "duration": 0.007719,
+ "end_time": "2020-10-02T07:38:07.814061",
"exception": false,
- "start_time": "2020-10-01T07:35:43.703116",
+ "start_time": "2020-10-02T07:38:07.806342",
"status": "completed"
},
"tags": []
@@ -297,10 +297,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 27.460067,
- "end_time": "2020-10-01T07:36:11.177520",
+ "duration": 26.639647,
+ "end_time": "2020-10-02T07:38:34.460276",
"exception": false,
- "start_time": "2020-10-01T07:35:43.717453",
+ "start_time": "2020-10-02T07:38:07.820629",
"status": "completed"
},
"tags": []
@@ -317,10 +317,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.045457,
- "end_time": "2020-10-01T07:36:11.242417",
+ "duration": 0.045923,
+ "end_time": "2020-10-02T07:38:34.525196",
"exception": false,
- "start_time": "2020-10-01T07:36:11.196960",
+ "start_time": "2020-10-02T07:38:34.479273",
"status": "completed"
},
"tags": []
@@ -339,10 +339,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.563513,
- "end_time": "2020-10-01T07:36:11.822084",
+ "duration": 0.702638,
+ "end_time": "2020-10-02T07:38:35.242651",
"exception": false,
- "start_time": "2020-10-01T07:36:11.258571",
+ "start_time": "2020-10-02T07:38:34.540013",
"status": "completed"
},
"tags": []
@@ -352,7 +352,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "11802 data points\n"
+ "11858 data points\n"
]
},
{
@@ -402,21 +402,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200930</td>\n",
+ " <td>20201001</td>\n",
" <td>AK</td>\n",
- " <td>8780.0</td>\n",
- " <td>448427.0</td>\n",
+ " <td>8912.0</td>\n",
+ " <td>453411.0</td>\n",
" <td>NaN</td>\n",
- " <td>457207.0</td>\n",
- " <td>53.0</td>\n",
+ " <td>462323.0</td>\n",
+ " <td>42.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>457207</td>\n",
- " <td>0</td>\n",
+ " <td>462323</td>\n",
+ " <td>1</td>\n",
" <td>0</td>\n",
- " <td>1716aba4b705ff74814829d25487c6e57d27122d</td>\n",
+ " <td>6fce5edde2805fba8ccfabc0232b39bb079a0c0a</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>20200930</td>\n",
+ " <td>20201001</td>\n",
" <td>AL</td>\n",
- " <td>154701.0</td>\n",
- " <td>994475.0</td>\n",
+ " <td>155744.0</td>\n",
+ " <td>1000570.0</td>\n",
" <td>NaN</td>\n",
- " <td>1132039.0</td>\n",
- " <td>776.0</td>\n",
+ " <td>1138732.0</td>\n",
+ " <td>760.0</td>\n",
" <td>17257.0</td>\n",
" <td>NaN</td>\n",
- " <td>1815.0</td>\n",
+ " <td>1832.0</td>\n",
" <td>...</td>\n",
- " <td>1149176</td>\n",
- " <td>23</td>\n",
- " <td>75</td>\n",
- " <td>6ec6077978a7573b69eb4da4ba7236140c79abd6</td>\n",
+ " <td>1156314</td>\n",
+ " <td>8</td>\n",
+ " <td>0</td>\n",
+ " <td>d7277459136bf4c2075ceaea9cd64c6a193a9e80</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -454,21 +454,21 @@
"</div>"
],
"text/plain": [
- " date state positive negative pending totalTestResults \\\n",
- "0 20200930 AK 8780.0 448427.0 NaN 457207.0 \n",
- "1 20200930 AL 154701.0 994475.0 NaN 1132039.0 \n",
+ " date state positive negative pending totalTestResults \\\n",
+ "0 20201001 AK 8912.0 453411.0 NaN 462323.0 \n",
+ "1 20201001 AL 155744.0 1000570.0 NaN 1138732.0 \n",
"\n",
" hospitalizedCurrently hospitalizedCumulative inIcuCurrently \\\n",
- "0 53.0 NaN NaN \n",
- "1 776.0 17257.0 NaN \n",
+ "0 42.0 NaN NaN \n",
+ "1 760.0 17257.0 NaN \n",
"\n",
" inIcuCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 NaN ... 457207 0 0 \n",
- "1 1815.0 ... 1149176 23 75 \n",
+ "0 NaN ... 462323 1 0 \n",
+ "1 1832.0 ... 1156314 8 0 \n",
"\n",
" hash commercialScore \\\n",
- "0 1716aba4b705ff74814829d25487c6e57d27122d 0 \n",
- "1 6ec6077978a7573b69eb4da4ba7236140c79abd6 0 \n",
+ "0 6fce5edde2805fba8ccfabc0232b39bb079a0c0a 0 \n",
+ "1 d7277459136bf4c2075ceaea9cd64c6a193a9e80 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": 37.262835,
- "end_time": "2020-10-01T07:36:12.252618",
+ "duration": 34.808625,
+ "end_time": "2020-10-02T07:38:35.670354",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/85owm2w1/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/el6ip4bh/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/85owm2w1/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/el6ip4bh/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-10-01T07:35:34.989783",
+ "start_time": "2020-10-02T07:38:00.861729",
"version": "1.1.0"
}
},