From 6342f3d1568164a18e12e83d197eae1a85fc8b6c Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Sat, 24 Oct 2020 07:53:50 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../6b10d269019247ac92c15ed8059eafe5.cwl | 120 ++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 132 +++++++++---------
4 files changed, 190 insertions(+), 70 deletions(-)
create mode 100644 .renku/workflow/6b10d269019247ac92c15ed8059eafe5.cwl
diff --git a/.renku/workflow/6b10d269019247ac92c15ed8059eafe5.cwl b/.renku/workflow/6b10d269019247ac92c15ed8059eafe5.cwl
new file mode 100644
index 000000000..d2f1ef920
--- /dev/null
+++ b/.renku/workflow/6b10d269019247ac92c15ed8059eafe5.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_1:
+ 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 88a1171e8..7f38a010c 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:cc1951cf29338ae3781e64ce3e44b914afbcff5f9f82f8d76a86af13d0aa3d4d
-size 17741097
+oid sha256:16682d903ed8a6b0ccf4ca43afd355faa7b7ce5aba1c5b503222b90c5303496e
+size 17818101
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index fe888f2dd..0362e76fc 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 sha256:90a8f3cf30ab857f2b8de9d26b067069da67ee076ab1db406384ef730875276e
-size 102208
+oid sha256:f90646fc532386199074033947a8e0e0cff4125da706f1a1dc99e9ddcf3f8095
+size 102172
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index e2a8297d5..d568f1063 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": 1.962235,
- "end_time": "2020-10-23T07:37:58.522239",
+ "duration": 3.520049,
+ "end_time": "2020-10-24T07:53:17.756990",
"exception": false,
- "start_time": "2020-10-23T07:37:56.560004",
+ "start_time": "2020-10-24T07:53:14.236941",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.020829,
- "end_time": "2020-10-23T07:37:58.554682",
+ "duration": 0.027464,
+ "end_time": "2020-10-24T07:53:17.801073",
"exception": false,
- "start_time": "2020-10-23T07:37:58.533853",
+ "start_time": "2020-10-24T07:53:17.773609",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.019996,
- "end_time": "2020-10-23T07:37:58.585100",
+ "duration": 0.02419,
+ "end_time": "2020-10-24T07:53:17.836826",
"exception": false,
- "start_time": "2020-10-23T07:37:58.565104",
+ "start_time": "2020-10-24T07:53:17.812636",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/zg6n4sh4/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/ni4orh0_/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": 0.008217,
- "end_time": "2020-10-23T07:37:58.602492",
+ "duration": 0.007658,
+ "end_time": "2020-10-24T07:53:17.852212",
"exception": false,
- "start_time": "2020-10-23T07:37:58.594275",
+ "start_time": "2020-10-24T07:53:17.844554",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.617892,
- "end_time": "2020-10-23T07:37:59.227842",
+ "duration": 0.617007,
+ "end_time": "2020-10-24T07:53:18.474980",
"exception": false,
- "start_time": "2020-10-23T07:37:58.609950",
+ "start_time": "2020-10-24T07:53:17.857973",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.024942,
- "end_time": "2020-10-23T07:37:59.264805",
+ "duration": 0.029508,
+ "end_time": "2020-10-24T07:53:18.520364",
"exception": false,
- "start_time": "2020-10-23T07:37:59.239863",
+ "start_time": "2020-10-24T07:53:18.490856",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.087278,
- "end_time": "2020-10-23T07:37:59.362274",
+ "duration": 0.075423,
+ "end_time": "2020-10-24T07:53:18.606156",
"exception": false,
- "start_time": "2020-10-23T07:37:59.274996",
+ "start_time": "2020-10-24T07:53:18.530733",
"status": "completed"
},
"tags": []
@@ -280,10 +280,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008876,
- "end_time": "2020-10-23T07:37:59.380337",
+ "duration": 0.008246,
+ "end_time": "2020-10-24T07:53:18.628357",
"exception": false,
- "start_time": "2020-10-23T07:37:59.371461",
+ "start_time": "2020-10-24T07:53:18.620111",
"status": "completed"
},
"tags": []
@@ -297,10 +297,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 29.670971,
- "end_time": "2020-10-23T07:38:29.059459",
+ "duration": 29.719818,
+ "end_time": "2020-10-24T07:53:48.355673",
"exception": false,
- "start_time": "2020-10-23T07:37:59.388488",
+ "start_time": "2020-10-24T07:53:18.635855",
"status": "completed"
},
"tags": []
@@ -317,10 +317,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.061755,
- "end_time": "2020-10-23T07:38:29.137194",
+ "duration": 0.067044,
+ "end_time": "2020-10-24T07:53:48.440245",
"exception": false,
- "start_time": "2020-10-23T07:38:29.075439",
+ "start_time": "2020-10-24T07:53:48.373201",
"status": "completed"
},
"tags": []
@@ -339,10 +339,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.721162,
- "end_time": "2020-10-23T07:38:29.869972",
+ "duration": 0.658594,
+ "end_time": "2020-10-24T07:53:49.114333",
"exception": false,
- "start_time": "2020-10-23T07:38:29.148810",
+ "start_time": "2020-10-24T07:53:48.455739",
"status": "completed"
},
"tags": []
@@ -352,7 +352,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "13045 data points\n"
+ "13101 data points\n"
]
},
{
@@ -402,21 +402,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201022</td>\n",
+ " <td>20201023</td>\n",
" <td>AK</td>\n",
- " <td>12877.0</td>\n",
+ " <td>13161.0</td>\n",
" <td>NaN</td>\n",
- " <td>535832.0</td>\n",
+ " <td>539585.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>548709.0</td>\n",
- " <td>41.0</td>\n",
+ " <td>552746.0</td>\n",
+ " <td>59.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>548709</td>\n",
+ " <td>552746</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
- " <td>28c731e31dacc3059dc3484060ecfc4139686eff</td>\n",
+ " <td>1b73fb16c097754ce2024af0e49f9d9514248af0</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>20201022</td>\n",
+ " <td>20201023</td>\n",
" <td>AL</td>\n",
- " <td>177064.0</td>\n",
- " <td>22122.0</td>\n",
- " <td>1125753.0</td>\n",
+ " <td>180916.0</td>\n",
+ " <td>25001.0</td>\n",
+ " <td>1133858.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1280695.0</td>\n",
- " <td>864.0</td>\n",
- " <td>19448.0</td>\n",
+ " <td>1289773.0</td>\n",
+ " <td>888.0</td>\n",
+ " <td>19595.0</td>\n",
" <td>...</td>\n",
- " <td>1302817</td>\n",
- " <td>38</td>\n",
- " <td>118</td>\n",
- " <td>711dab0898001c282a21f6187be2facd875da1d2</td>\n",
+ " <td>1314774</td>\n",
+ " <td>16</td>\n",
+ " <td>147</td>\n",
+ " <td>5323772280706f0dd467c842b6640d6f931d3c5a</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 20201022 AK 12877.0 NaN 535832.0 NaN \n",
- "1 20201022 AL 177064.0 22122.0 1125753.0 NaN \n",
+ "0 20201023 AK 13161.0 NaN 539585.0 NaN \n",
+ "1 20201023 AL 180916.0 25001.0 1133858.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 548709.0 41.0 \n",
- "1 totalTestsViral 1280695.0 864.0 \n",
+ "0 totalTestsViral 552746.0 59.0 \n",
+ "1 totalTestsViral 1289773.0 888.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 NaN ... 548709 0 0 \n",
- "1 19448.0 ... 1302817 38 118 \n",
+ "0 NaN ... 552746 0 0 \n",
+ "1 19595.0 ... 1314774 16 147 \n",
"\n",
" hash commercialScore \\\n",
- "0 28c731e31dacc3059dc3484060ecfc4139686eff 0 \n",
- "1 711dab0898001c282a21f6187be2facd875da1d2 0 \n",
+ "0 1b73fb16c097754ce2024af0e49f9d9514248af0 0 \n",
+ "1 5323772280706f0dd467c842b6640d6f931d3c5a 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": 35.259298,
- "end_time": "2020-10-23T07:38:30.199215",
+ "duration": 37.048735,
+ "end_time": "2020-10-24T07:53:49.543034",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/zg6n4sh4/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/ni4orh0_/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/zg6n4sh4/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/ni4orh0_/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-10-23T07:37:54.939917",
+ "start_time": "2020-10-24T07:53:12.494299",
"version": "1.1.0"
}
},
--
GitLab