diff --git a/.renku/workflow/db6c2fe5b1f44106bc265c2928eeca5e.cwl b/.renku/workflow/db6c2fe5b1f44106bc265c2928eeca5e.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..4c042a796eb6371d0cbf0207a26898e8de4d3413
--- /dev/null
+++ b/.renku/workflow/db6c2fe5b1f44106bc265c2928eeca5e.cwl
@@ -0,0 +1,148 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: states-daily.json
+ streamable: false
+ type: string
+ input_10:
+ default: states-metadata.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: out_folder
+ streamable: false
+ type: string
+ input_7:
+ default: data/covidtracking
+ streamable: false
+ type: string
+ input_8:
+ default:
+ class: File
+ path: ../../notebooks/process/download-covidtracking-data.ipynb
+ streamable: false
+ type: File
+ input_9:
+ default: runs/download-covidtracking-data.runs.ipynb
+ streamable: false
+ type: string
+outputs:
+ output_0:
+ outputSource: step_2/output_1
+ streamable: false
+ type: Directory
+ output_2:
+ outputSource: step_2/output_0
+ streamable: false
+ type: File
+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-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:
+ input_1: input_6
+ input_2: input_7
+ input_3: input_8
+ input_4: input_9
+ out:
+ - output_0
+ - output_1
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
+ step_4:
+ in:
+ filename: input_10
+ 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 5163fa67705c919d9c516bb5cc88cc18a235d587..c39e7cb93cd9b2e8dabda54c0e28ac5900c24a01 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 sha256:49daa3567fbddb38f172831d9a251fdf13847222e00514f939f8b237a65b05cd
-size 430713
+oid sha256:620d7a5960bd2efd7502001d04f38d2cf630a5937e9b5b30ee59edecab5b7a3a
+size 451064
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 3e63c62941ff156f8e95f8ce0f1522ae00ead654..f3ede08085838e9f0060fc88168e3e6a24620316 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:a2de8c05ab448b3f0eb44787afeb88b313332f50271c9a76bba6c7949ee90520
-size 27083
+oid sha256:9ee2bb71091d1976a748e75088484a079c32f959736aefb777262beef24b71d5
+size 25321
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 93cbcae5c2d4607e36101aa9a75820b95d6edf60..f64569502a12438646fd6e18212f3b4bb56a8b2c 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": 4.191695,
- "end_time": "2020-03-28T20:12:31.515945",
+ "duration": 0.466467,
+ "end_time": "2020-03-29T08:22:31.907089",
"exception": false,
- "start_time": "2020-03-28T20:12:27.324250",
+ "start_time": "2020-03-29T08:22:31.440622",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.017506,
- "end_time": "2020-03-28T20:12:31.548018",
+ "duration": 0.018031,
+ "end_time": "2020-03-29T08:22:31.938653",
"exception": false,
- "start_time": "2020-03-28T20:12:31.530512",
+ "start_time": "2020-03-29T08:22:31.920622",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.013182,
- "end_time": "2020-03-28T20:12:31.569039",
+ "duration": 0.018359,
+ "end_time": "2020-03-29T08:22:31.964788",
"exception": false,
- "start_time": "2020-03-28T20:12:31.555857",
+ "start_time": "2020-03-29T08:22:31.946429",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/wjmbqwda/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/bdf81mi5/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": 0.005359,
- "end_time": "2020-03-28T20:12:31.579757",
+ "duration": 0.008065,
+ "end_time": "2020-03-29T08:22:31.981763",
"exception": false,
- "start_time": "2020-03-28T20:12:31.574398",
+ "start_time": "2020-03-29T08:22:31.973698",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.245025,
- "end_time": "2020-03-28T20:12:31.830246",
+ "duration": 0.063028,
+ "end_time": "2020-03-29T08:22:32.052258",
"exception": false,
- "start_time": "2020-03-28T20:12:31.585221",
+ "start_time": "2020-03-29T08:22:31.989230",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.022778,
- "end_time": "2020-03-28T20:12:31.866438",
+ "duration": 0.020595,
+ "end_time": "2020-03-29T08:22:32.084858",
"exception": false,
- "start_time": "2020-03-28T20:12:31.843660",
+ "start_time": "2020-03-29T08:22:32.064263",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.047291,
- "end_time": "2020-03-28T20:12:31.922933",
+ "duration": 0.062439,
+ "end_time": "2020-03-29T08:22:32.156029",
"exception": false,
- "start_time": "2020-03-28T20:12:31.875642",
+ "start_time": "2020-03-29T08:22:32.093590",
"status": "completed"
},
"tags": []
@@ -201,7 +201,7 @@
" <td>@alpublichealth</td>\n",
" <td>No data</td>\n",
" <td>False</td>\n",
- " <td>Negatives = Totals - Positives. Positives seem...</td>\n",
+ " <td>Negatives = (Totals - Positives) \\nPositives o...</td>\n",
" <td>1</td>\n",
" <td>Alabama</td>\n",
" </tr>\n",
@@ -224,7 +224,7 @@
"\n",
" pui pum notes fips \\\n",
"0 All data False Total tests are taken from the annotations on ... 2 \n",
- "1 No data False Negatives = Totals - Positives. Positives seem... 1 \n",
+ "1 No data False Negatives = (Totals - Positives) \\nPositives o... 1 \n",
"\n",
" name \n",
"0 Alaska \n",
@@ -246,10 +246,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.006017,
- "end_time": "2020-03-28T20:12:31.935616",
+ "duration": 0.007936,
+ "end_time": "2020-03-29T08:22:32.175985",
"exception": false,
- "start_time": "2020-03-28T20:12:31.929599",
+ "start_time": "2020-03-29T08:22:32.168049",
"status": "completed"
},
"tags": []
@@ -263,10 +263,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.22026,
- "end_time": "2020-03-28T20:12:32.162099",
+ "duration": 0.16391,
+ "end_time": "2020-03-29T08:22:32.348092",
"exception": false,
- "start_time": "2020-03-28T20:12:31.941839",
+ "start_time": "2020-03-29T08:22:32.184182",
"status": "completed"
},
"tags": []
@@ -283,10 +283,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.024935,
- "end_time": "2020-03-28T20:12:32.202190",
+ "duration": 0.021284,
+ "end_time": "2020-03-29T08:22:32.380284",
"exception": false,
- "start_time": "2020-03-28T20:12:32.177255",
+ "start_time": "2020-03-29T08:22:32.359000",
"status": "completed"
},
"tags": []
@@ -305,10 +305,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.067003,
- "end_time": "2020-03-28T20:12:32.277906",
+ "duration": 0.076359,
+ "end_time": "2020-03-29T08:22:32.467959",
"exception": false,
- "start_time": "2020-03-28T20:12:32.210903",
+ "start_time": "2020-03-29T08:22:32.391600",
"status": "completed"
},
"tags": []
@@ -318,7 +318,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "1205 data points\n"
+ "1261 data points\n"
]
},
{
@@ -364,43 +364,43 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200327</td>\n",
+ " <td>20200328</td>\n",
" <td>AK</td>\n",
- " <td>69.0</td>\n",
- " <td>2319.0</td>\n",
- " <td>13.0</td>\n",
- " <td>3.0</td>\n",
- " <td>1.0</td>\n",
- " <td>2401</td>\n",
- " <td>588f633d59494e4d58466fccfa9628c98568396b</td>\n",
- " <td>2020-03-27T20:00:00Z</td>\n",
- " <td>2388</td>\n",
+ " <td>85.0</td>\n",
+ " <td>2836.0</td>\n",
+ " <td>NaN</td>\n",
+ " <td>5.0</td>\n",
+ " <td>2.0</td>\n",
+ " <td>2921</td>\n",
+ " <td>edb7e6bcde715f8bbea31547e99aa8b4712ea5fb</td>\n",
+ " <td>2020-03-28T20:00:00Z</td>\n",
+ " <td>2921</td>\n",
" <td>2</td>\n",
- " <td>0.0</td>\n",
- " <td>0.0</td>\n",
- " <td>518.0</td>\n",
- " <td>10.0</td>\n",
- " <td>528.0</td>\n",
+ " <td>1.0</td>\n",
+ " <td>2.0</td>\n",
+ " <td>517.0</td>\n",
+ " <td>16.0</td>\n",
+ " <td>533.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200327</td>\n",
+ " <td>20200328</td>\n",
" <td>AL</td>\n",
- " <td>587.0</td>\n",
+ " <td>696.0</td>\n",
" <td>4184.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>3.0</td>\n",
- " <td>4771</td>\n",
- " <td>c3883f10c8760fdd9d196c5e2483205434bc4e0f</td>\n",
- " <td>2020-03-27T20:00:00Z</td>\n",
- " <td>4771</td>\n",
+ " <td>4880</td>\n",
+ " <td>c9986a845bd2f8f9c9a4294a8e5d66a01ee6aadf</td>\n",
+ " <td>2020-03-28T20:00:00Z</td>\n",
+ " <td>4880</td>\n",
" <td>1</td>\n",
- " <td>2.0</td>\n",
" <td>0.0</td>\n",
- " <td>591.0</td>\n",
- " <td>81.0</td>\n",
- " <td>672.0</td>\n",
+ " <td>0.0</td>\n",
+ " <td>0.0</td>\n",
+ " <td>109.0</td>\n",
+ " <td>109.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
@@ -408,20 +408,20 @@
],
"text/plain": [
" date state positive negative pending hospitalized death total \\\n",
- "0 20200327 AK 69.0 2319.0 13.0 3.0 1.0 2401 \n",
- "1 20200327 AL 587.0 4184.0 NaN NaN 3.0 4771 \n",
+ "0 20200328 AK 85.0 2836.0 NaN 5.0 2.0 2921 \n",
+ "1 20200328 AL 696.0 4184.0 NaN NaN 3.0 4880 \n",
"\n",
" hash dateChecked \\\n",
- "0 588f633d59494e4d58466fccfa9628c98568396b 2020-03-27T20:00:00Z \n",
- "1 c3883f10c8760fdd9d196c5e2483205434bc4e0f 2020-03-27T20:00:00Z \n",
+ "0 edb7e6bcde715f8bbea31547e99aa8b4712ea5fb 2020-03-28T20:00:00Z \n",
+ "1 c9986a845bd2f8f9c9a4294a8e5d66a01ee6aadf 2020-03-28T20:00:00Z \n",
"\n",
" totalTestResults fips deathIncrease hospitalizedIncrease \\\n",
- "0 2388 2 0.0 0.0 \n",
- "1 4771 1 2.0 0.0 \n",
+ "0 2921 2 1.0 2.0 \n",
+ "1 4880 1 0.0 0.0 \n",
"\n",
" negativeIncrease positiveIncrease totalTestResultsIncrease \n",
- "0 518.0 10.0 528.0 \n",
- "1 591.0 81.0 672.0 "
+ "0 517.0 16.0 533.0 \n",
+ "1 0.0 109.0 109.0 "
]
},
"execution_count": 9,
@@ -455,18 +455,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 6.835148,
- "end_time": "2020-03-28T20:12:32.619791",
+ "duration": 2.185859,
+ "end_time": "2020-03-29T08:22:32.791063",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/wjmbqwda/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/bdf81mi5/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/wjmbqwda/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/bdf81mi5/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-03-28T20:12:25.784643",
+ "start_time": "2020-03-29T08:22:30.605204",
"version": "1.1.0"
}
},