From 01ec83027a1a60d7fdc43bbcbe1ed1589f145872 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <cramakri+covid-cron@ethz.ch>
Date: Thu, 23 Apr 2020 07:25:44 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../056013780b0849118b7789497cc14c9c.cwl | 148 ++++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 144 ++++++++---------
4 files changed, 224 insertions(+), 76 deletions(-)
create mode 100644 .renku/workflow/056013780b0849118b7789497cc14c9c.cwl
diff --git a/.renku/workflow/056013780b0849118b7789497cc14c9c.cwl b/.renku/workflow/056013780b0849118b7789497cc14c9c.cwl
new file mode 100644
index 000000000..247d32bc6
--- /dev/null
+++ b/.renku/workflow/056013780b0849118b7789497cc14c9c.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_2:
+ 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:
+ 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_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
+ - *id002
+ successCodes: []
+ temporaryFailCodes: []
diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index 2268880a1..fa3abf56e 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 sha256:2741616ce804f09a57e91994eefddf08b69f19d61650fd654ebd5f791bb69fe1
-size 1296997
+oid sha256:fe0159a2a71ff0d1fb1826d3b7c64a5521a43bae971d6f7a53251aef16a98aa7
+size 1332057
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 91869fdd0..92cfc8271 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:e09dc92ab8fd8ee1b8f62d98ab273afb13132e32eac757e6ee4128e6c5d975f3
-size 28635
+oid sha256:a602301962982474d3e6c3e609022b94dff92782a0af644cd98008bc17521de5
+size 28757
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index d69566477..43c4d395e 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": 0.537757,
- "end_time": "2020-04-22T07:26:03.736336",
+ "duration": 1.60642,
+ "end_time": "2020-04-23T07:25:39.761433",
"exception": false,
- "start_time": "2020-04-22T07:26:03.198579",
+ "start_time": "2020-04-23T07:25:38.155013",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.025946,
- "end_time": "2020-04-22T07:26:03.774138",
+ "duration": 0.027358,
+ "end_time": "2020-04-23T07:25:39.808543",
"exception": false,
- "start_time": "2020-04-22T07:26:03.748192",
+ "start_time": "2020-04-23T07:25:39.781185",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.02433,
- "end_time": "2020-04-22T07:26:03.813292",
+ "duration": 0.023119,
+ "end_time": "2020-04-23T07:25:39.841604",
"exception": false,
- "start_time": "2020-04-22T07:26:03.788962",
+ "start_time": "2020-04-23T07:25:39.818485",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/vwmf0jau/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/5uveaykp/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": 0.007982,
- "end_time": "2020-04-22T07:26:03.830058",
+ "duration": 0.006677,
+ "end_time": "2020-04-23T07:25:39.855331",
"exception": false,
- "start_time": "2020-04-22T07:26:03.822076",
+ "start_time": "2020-04-23T07:25:39.848654",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.255316,
- "end_time": "2020-04-22T07:26:04.091234",
+ "duration": 0.157191,
+ "end_time": "2020-04-23T07:25:40.018550",
"exception": false,
- "start_time": "2020-04-22T07:26:03.835918",
+ "start_time": "2020-04-23T07:25:39.861359",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.026576,
- "end_time": "2020-04-22T07:26:04.132325",
+ "duration": 0.028598,
+ "end_time": "2020-04-23T07:25:40.061751",
"exception": false,
- "start_time": "2020-04-22T07:26:04.105749",
+ "start_time": "2020-04-23T07:25:40.033153",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.07693,
- "end_time": "2020-04-22T07:26:04.218750",
+ "duration": 0.073297,
+ "end_time": "2020-04-23T07:25:40.148737",
"exception": false,
- "start_time": "2020-04-22T07:26:04.141820",
+ "start_time": "2020-04-23T07:25:40.075440",
"status": "completed"
},
"tags": []
@@ -246,10 +246,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008348,
- "end_time": "2020-04-22T07:26:04.240058",
+ "duration": 0.007835,
+ "end_time": "2020-04-23T07:25:40.168710",
"exception": false,
- "start_time": "2020-04-22T07:26:04.231710",
+ "start_time": "2020-04-23T07:25:40.160875",
"status": "completed"
},
"tags": []
@@ -263,10 +263,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.313441,
- "end_time": "2020-04-22T07:26:04.560698",
+ "duration": 0.249515,
+ "end_time": "2020-04-23T07:25:40.424452",
"exception": false,
- "start_time": "2020-04-22T07:26:04.247257",
+ "start_time": "2020-04-23T07:25:40.174937",
"status": "completed"
},
"tags": []
@@ -283,10 +283,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.034309,
- "end_time": "2020-04-22T07:26:04.610677",
+ "duration": 0.031698,
+ "end_time": "2020-04-23T07:25:40.471178",
"exception": false,
- "start_time": "2020-04-22T07:26:04.576368",
+ "start_time": "2020-04-23T07:25:40.439480",
"status": "completed"
},
"tags": []
@@ -305,10 +305,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.123985,
- "end_time": "2020-04-22T07:26:04.751067",
+ "duration": 0.118394,
+ "end_time": "2020-04-23T07:25:40.602114",
"exception": false,
- "start_time": "2020-04-22T07:26:04.627082",
+ "start_time": "2020-04-23T07:25:40.483720",
"status": "completed"
},
"tags": []
@@ -318,7 +318,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "2620 data points\n"
+ "2676 data points\n"
]
},
{
@@ -368,51 +368,51 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200421</td>\n",
+ " <td>20200422</td>\n",
" <td>AK</td>\n",
- " <td>329.0</td>\n",
- " <td>10790.0</td>\n",
+ " <td>335.0</td>\n",
+ " <td>11824.0</td>\n",
" <td>NaN</td>\n",
- " <td>42.0</td>\n",
+ " <td>39.0</td>\n",
" <td>36.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
" <td>36.0</td>\n",
- " <td>11119.0</td>\n",
- " <td>11119.0</td>\n",
- " <td>11119.0</td>\n",
+ " <td>12159.0</td>\n",
+ " <td>12159.0</td>\n",
+ " <td>12159.0</td>\n",
" <td>2</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
- " <td>987.0</td>\n",
- " <td>8.0</td>\n",
- " <td>995.0</td>\n",
+ " <td>1034.0</td>\n",
+ " <td>6.0</td>\n",
+ " <td>1040.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200421</td>\n",
+ " <td>20200422</td>\n",
" <td>AL</td>\n",
- " <td>5231.0</td>\n",
+ " <td>5465.0</td>\n",
" <td>43295.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>699.0</td>\n",
+ " <td>730.0</td>\n",
" <td>NaN</td>\n",
- " <td>260.0</td>\n",
+ " <td>288.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>699.0</td>\n",
- " <td>48526.0</td>\n",
- " <td>48526.0</td>\n",
- " <td>48526.0</td>\n",
+ " <td>730.0</td>\n",
+ " <td>48760.0</td>\n",
+ " <td>48760.0</td>\n",
+ " <td>48760.0</td>\n",
" <td>1</td>\n",
- " <td>10.0</td>\n",
- " <td>58.0</td>\n",
- " <td>2420.0</td>\n",
- " <td>206.0</td>\n",
- " <td>2626.0</td>\n",
+ " <td>17.0</td>\n",
+ " <td>31.0</td>\n",
+ " <td>0.0</td>\n",
+ " <td>234.0</td>\n",
+ " <td>234.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
@@ -421,24 +421,24 @@
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200421 AK 329.0 10790.0 NaN 42.0 \n",
- "1 20200421 AL 5231.0 43295.0 NaN NaN \n",
+ "0 20200422 AK 335.0 11824.0 NaN 39.0 \n",
+ "1 20200422 AL 5465.0 43295.0 NaN NaN \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 36.0 NaN NaN \n",
- "1 699.0 NaN 260.0 \n",
+ "1 730.0 NaN 288.0 \n",
"\n",
" onVentilatorCurrently ... hospitalized total totalTestResults \\\n",
- "0 NaN ... 36.0 11119.0 11119.0 \n",
- "1 NaN ... 699.0 48526.0 48526.0 \n",
+ "0 NaN ... 36.0 12159.0 12159.0 \n",
+ "1 NaN ... 730.0 48760.0 48760.0 \n",
"\n",
" posNeg fips deathIncrease hospitalizedIncrease negativeIncrease \\\n",
- "0 11119.0 2 0.0 0.0 987.0 \n",
- "1 48526.0 1 10.0 58.0 2420.0 \n",
+ "0 12159.0 2 0.0 0.0 1034.0 \n",
+ "1 48760.0 1 17.0 31.0 0.0 \n",
"\n",
" positiveIncrease totalTestResultsIncrease \n",
- "0 8.0 995.0 \n",
- "1 206.0 2626.0 \n",
+ "0 6.0 1040.0 \n",
+ "1 234.0 234.0 \n",
"\n",
"[2 rows x 25 columns]"
]
@@ -474,18 +474,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 3.020416,
- "end_time": "2020-04-22T07:26:05.182696",
+ "duration": 3.812008,
+ "end_time": "2020-04-23T07:25:40.931308",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/vwmf0jau/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/5uveaykp/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/vwmf0jau/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/5uveaykp/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-04-22T07:26:02.162280",
+ "start_time": "2020-04-23T07:25:37.119300",
"version": "1.1.0"
}
},
--
GitLab