From e6d18d597b48b3d467b31e84997709c06d7923a0 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <cramakri+covid-cron@ethz.ch>
Date: Sat, 21 Mar 2020 21:18:12 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../ff8c6fc2e792427ab1d73080601a9b4e.cwl | 148 ++++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 87 +++++-----
4 files changed, 197 insertions(+), 46 deletions(-)
create mode 100644 .renku/workflow/ff8c6fc2e792427ab1d73080601a9b4e.cwl
diff --git a/.renku/workflow/ff8c6fc2e792427ab1d73080601a9b4e.cwl b/.renku/workflow/ff8c6fc2e792427ab1d73080601a9b4e.cwl
new file mode 100644
index 00000000..8a5ca753
--- /dev/null
+++ b/.renku/workflow/ff8c6fc2e792427ab1d73080601a9b4e.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: runs/download-covidtracking-data.runs.ipynb
+ streamable: false
+ type: string
+ input_2:
+ default: states-metadata.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
+ input_7:
+ default: out_folder
+ streamable: false
+ type: string
+ input_8:
+ default: data/covidtracking
+ streamable: false
+ type: string
+ input_9:
+ default:
+ class: File
+ path: ../../notebooks/process/download-covidtracking-data.ipynb
+ streamable: false
+ type: File
+outputs:
+ output_0:
+ outputSource: step_3/output_0
+ streamable: false
+ type: File
+ output_1:
+ 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-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:
+ filename: input_2
+ input_directory: step_4/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: []
+ step_3:
+ in:
+ input_1: input_3
+ input_2: input_4
+ input_3: input_5
+ input_4: input_6
+ out:
+ - output_0
+ - output_1
+ run: ff5f474d38144c5d882c0036bd1059c2_papermill.cwl
+ step_4:
+ in:
+ input_1: input_7
+ input_2: input_8
+ input_3: input_9
+ input_4: input_10
+ out:
+ - output_0
+ - output_1
+ run: ff5f474d38144c5d882c0036bd1059c2_papermill.cwl
diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index f2d6a22d..e1a247a7 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 sha256:9dd4d36f37d438f6cd6f77857cbd7cfbcc50bd154dcfe661b82f7b3cfbf04292
-size 109274
+oid sha256:a77694fad0e5a3535a958885f2411ce55bfad90d38d95b908360b69e2914255b
+size 125534
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index d47b2b85..57cba581 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 sha256:5089d92f8f1bd14af587fc85dacb53cd78da406490db554e06e5390bb3c78e49
-size 25096
+oid sha256:ad39d5a2d631281cda4edbb6b660556bf8ac46a1c12520a9106b53b7d43c9a0c
+size 25673
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index d42f03dc..070806c9 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": 0.629269,
- "end_time": "2020-03-21T08:20:57.267554",
+ "duration": 3.807963,
+ "end_time": "2020-03-21T21:18:07.631574",
"exception": false,
- "start_time": "2020-03-21T08:20:56.638285",
+ "start_time": "2020-03-21T21:18:03.823611",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.02649,
- "end_time": "2020-03-21T08:20:57.303536",
+ "duration": 0.019935,
+ "end_time": "2020-03-21T21:18:07.664678",
"exception": false,
- "start_time": "2020-03-21T08:20:57.277046",
+ "start_time": "2020-03-21T21:18:07.644743",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.028563,
- "end_time": "2020-03-21T08:20:57.341818",
+ "duration": 0.021741,
+ "end_time": "2020-03-21T21:18:07.695982",
"exception": false,
- "start_time": "2020-03-21T08:20:57.313255",
+ "start_time": "2020-03-21T21:18:07.674241",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/3mmsluiy/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/397wwqxv/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": 0.008049,
- "end_time": "2020-03-21T08:20:57.359485",
+ "duration": 0.008379,
+ "end_time": "2020-03-21T21:18:07.713115",
"exception": false,
- "start_time": "2020-03-21T08:20:57.351436",
+ "start_time": "2020-03-21T21:18:07.704736",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.485128,
- "end_time": "2020-03-21T08:20:57.851793",
+ "duration": 0.398279,
+ "end_time": "2020-03-21T21:18:08.119632",
"exception": false,
- "start_time": "2020-03-21T08:20:57.366665",
+ "start_time": "2020-03-21T21:18:07.721353",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.021648,
- "end_time": "2020-03-21T08:20:57.882047",
+ "duration": 0.023593,
+ "end_time": "2020-03-21T21:18:08.154644",
"exception": false,
- "start_time": "2020-03-21T08:20:57.860399",
+ "start_time": "2020-03-21T21:18:08.131051",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.062476,
- "end_time": "2020-03-21T08:20:57.953678",
+ "duration": 0.069188,
+ "end_time": "2020-03-21T21:18:08.235282",
"exception": false,
- "start_time": "2020-03-21T08:20:57.891202",
+ "start_time": "2020-03-21T21:18:08.166094",
"status": "completed"
},
"tags": []
@@ -239,10 +239,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007856,
- "end_time": "2020-03-21T08:20:57.970301",
+ "duration": 0.008146,
+ "end_time": "2020-03-21T21:18:08.252868",
"exception": false,
- "start_time": "2020-03-21T08:20:57.962445",
+ "start_time": "2020-03-21T21:18:08.244722",
"status": "completed"
},
"tags": []
@@ -256,10 +256,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.531499,
- "end_time": "2020-03-21T08:20:58.509641",
+ "duration": 0.136609,
+ "end_time": "2020-03-21T21:18:08.397510",
"exception": false,
- "start_time": "2020-03-21T08:20:57.978142",
+ "start_time": "2020-03-21T21:18:08.260901",
"status": "completed"
},
"tags": []
@@ -276,10 +276,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.025604,
- "end_time": "2020-03-21T08:20:58.549427",
+ "duration": 0.023235,
+ "end_time": "2020-03-21T21:18:08.431887",
"exception": false,
- "start_time": "2020-03-21T08:20:58.523823",
+ "start_time": "2020-03-21T21:18:08.408652",
"status": "completed"
},
"tags": []
@@ -298,10 +298,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.048458,
- "end_time": "2020-03-21T08:20:58.605911",
+ "duration": 0.059119,
+ "end_time": "2020-03-21T21:18:08.500951",
"exception": false,
- "start_time": "2020-03-21T08:20:58.557453",
+ "start_time": "2020-03-21T21:18:08.441832",
"status": "completed"
},
"tags": []
@@ -340,6 +340,7 @@
" <th>positive</th>\n",
" <th>negative</th>\n",
" <th>pending</th>\n",
+ " <th>hospitalized</th>\n",
" <th>death</th>\n",
" <th>total</th>\n",
" <th>dateChecked</th>\n",
@@ -354,6 +355,7 @@
" <td>686.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
+ " <td>NaN</td>\n",
" <td>698</td>\n",
" <td>2020-03-20T20:00:00Z</td>\n",
" </tr>\n",
@@ -364,6 +366,7 @@
" <td>81</td>\n",
" <td>28.0</td>\n",
" <td>NaN</td>\n",
+ " <td>NaN</td>\n",
" <td>0.0</td>\n",
" <td>109</td>\n",
" <td>2020-03-20T20:00:00Z</td>\n",
@@ -373,9 +376,9 @@
"</div>"
],
"text/plain": [
- " date state positive negative pending death total \\\n",
- "0 20200320 AK 12 686.0 NaN NaN 698 \n",
- "1 20200320 AL 81 28.0 NaN 0.0 109 \n",
+ " date state positive negative pending hospitalized death total \\\n",
+ "0 20200320 AK 12 686.0 NaN NaN NaN 698 \n",
+ "1 20200320 AL 81 28.0 NaN NaN 0.0 109 \n",
"\n",
" dateChecked \n",
"0 2020-03-20T20:00:00Z \n",
@@ -413,18 +416,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 3.207512,
- "end_time": "2020-03-21T08:20:58.929761",
+ "duration": 6.532057,
+ "end_time": "2020-03-21T21:18:08.825900",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/3mmsluiy/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/397wwqxv/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/3mmsluiy/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/397wwqxv/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-03-21T08:20:55.722249",
+ "start_time": "2020-03-21T21:18:02.293843",
"version": "1.1.0"
}
},
--
GitLab