From 3b2a6f1dd40cbf5bd1001deaab88d68a11380288 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <cramakri+covid-cron@ethz.ch>
Date: Sat, 21 Mar 2020 08:20:59 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../1de6e78bf529411d866f95d03aac54b6.cwl | 120 ++++++++++++++++++
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 78 ++++++------
3 files changed, 161 insertions(+), 41 deletions(-)
create mode 100644 .renku/workflow/1de6e78bf529411d866f95d03aac54b6.cwl
diff --git a/.renku/workflow/1de6e78bf529411d866f95d03aac54b6.cwl b/.renku/workflow/1de6e78bf529411d866f95d03aac54b6.cwl
new file mode 100644
index 0000000..90f0ced
--- /dev/null
+++ b/.renku/workflow/1de6e78bf529411d866f95d03aac54b6.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: 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-daily.json
+ 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_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
+ 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_1
+ - output_0
+ run: ff5f474d38144c5d882c0036bd1059c2_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-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: []
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 1f1aca4..d47b2b8 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 sha256:313f39a8ca639fbe07354929d7fa1350f81131a25f5650d4c16ce733a3349b9f
-size 24242
+oid sha256:5089d92f8f1bd14af587fc85dacb53cd78da406490db554e06e5390bb3c78e49
+size 25096
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index e80d21d..d42f03d 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": 3.757919,
- "end_time": "2020-03-20T21:45:29.726180",
+ "duration": 0.629269,
+ "end_time": "2020-03-21T08:20:57.267554",
"exception": false,
- "start_time": "2020-03-20T21:45:25.968261",
+ "start_time": "2020-03-21T08:20:56.638285",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.018354,
- "end_time": "2020-03-20T21:45:29.758115",
+ "duration": 0.02649,
+ "end_time": "2020-03-21T08:20:57.303536",
"exception": false,
- "start_time": "2020-03-20T21:45:29.739761",
+ "start_time": "2020-03-21T08:20:57.277046",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.021368,
- "end_time": "2020-03-20T21:45:29.787594",
+ "duration": 0.028563,
+ "end_time": "2020-03-21T08:20:57.341818",
"exception": false,
- "start_time": "2020-03-20T21:45:29.766226",
+ "start_time": "2020-03-21T08:20:57.313255",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/f3pmvx85/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/3mmsluiy/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": 0.008377,
- "end_time": "2020-03-20T21:45:29.807144",
+ "duration": 0.008049,
+ "end_time": "2020-03-21T08:20:57.359485",
"exception": false,
- "start_time": "2020-03-20T21:45:29.798767",
+ "start_time": "2020-03-21T08:20:57.351436",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.430485,
- "end_time": "2020-03-20T21:45:30.245726",
+ "duration": 0.485128,
+ "end_time": "2020-03-21T08:20:57.851793",
"exception": false,
- "start_time": "2020-03-20T21:45:29.815241",
+ "start_time": "2020-03-21T08:20:57.366665",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.021358,
- "end_time": "2020-03-20T21:45:30.277302",
+ "duration": 0.021648,
+ "end_time": "2020-03-21T08:20:57.882047",
"exception": false,
- "start_time": "2020-03-20T21:45:30.255944",
+ "start_time": "2020-03-21T08:20:57.860399",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.063279,
- "end_time": "2020-03-20T21:45:30.348415",
+ "duration": 0.062476,
+ "end_time": "2020-03-21T08:20:57.953678",
"exception": false,
- "start_time": "2020-03-20T21:45:30.285136",
+ "start_time": "2020-03-21T08:20:57.891202",
"status": "completed"
},
"tags": []
@@ -239,10 +239,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008215,
- "end_time": "2020-03-20T21:45:30.366192",
+ "duration": 0.007856,
+ "end_time": "2020-03-21T08:20:57.970301",
"exception": false,
- "start_time": "2020-03-20T21:45:30.357977",
+ "start_time": "2020-03-21T08:20:57.962445",
"status": "completed"
},
"tags": []
@@ -256,10 +256,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.658874,
- "end_time": "2020-03-20T21:45:31.033153",
+ "duration": 0.531499,
+ "end_time": "2020-03-21T08:20:58.509641",
"exception": false,
- "start_time": "2020-03-20T21:45:30.374279",
+ "start_time": "2020-03-21T08:20:57.978142",
"status": "completed"
},
"tags": []
@@ -276,10 +276,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.018873,
- "end_time": "2020-03-20T21:45:31.062632",
+ "duration": 0.025604,
+ "end_time": "2020-03-21T08:20:58.549427",
"exception": false,
- "start_time": "2020-03-20T21:45:31.043759",
+ "start_time": "2020-03-21T08:20:58.523823",
"status": "completed"
},
"tags": []
@@ -298,10 +298,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.053619,
- "end_time": "2020-03-20T21:45:31.127152",
+ "duration": 0.048458,
+ "end_time": "2020-03-21T08:20:58.605911",
"exception": false,
- "start_time": "2020-03-20T21:45:31.073533",
+ "start_time": "2020-03-21T08:20:58.557453",
"status": "completed"
},
"tags": []
@@ -413,18 +413,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 6.856589,
- "end_time": "2020-03-20T21:45:31.451326",
+ "duration": 3.207512,
+ "end_time": "2020-03-21T08:20:58.929761",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/f3pmvx85/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/3mmsluiy/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/f3pmvx85/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/3mmsluiy/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-03-20T21:45:24.594737",
+ "start_time": "2020-03-21T08:20:55.722249",
"version": "1.1.0"
}
},
--
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