From 8f4fa877e7743a22354701cc413a0597860d254d Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <cramakri+covid-cron@ethz.ch>
Date: Mon, 30 Mar 2020 19:54:12 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../2327ebf1e3d449bcb2552d1dfea7d718.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/2327ebf1e3d449bcb2552d1dfea7d718.cwl
diff --git a/.renku/workflow/2327ebf1e3d449bcb2552d1dfea7d718.cwl b/.renku/workflow/2327ebf1e3d449bcb2552d1dfea7d718.cwl
new file mode 100644
index 0000000..7e97654
--- /dev/null
+++ b/.renku/workflow/2327ebf1e3d449bcb2552d1dfea7d718.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_1:
+ 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: a17d560c41a54f5aa307ce5f3c5effe5_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 ce67df1..3acf4ba 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 sha256:306bc64b6fee54d73398efe54f01497474cbf76b0c2ddbd38a86f5a4652f8f46
-size 25348
+oid sha256:0f70a22f2cacc03590ce4e2be83e8af64cc64b863639fac327f07d32470c2213
+size 25750
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 1f78abb..9075747 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": 0.492815,
- "end_time": "2020-03-30T08:27:40.229411",
+ "duration": 0.895891,
+ "end_time": "2020-03-30T19:54:09.980998",
"exception": false,
- "start_time": "2020-03-30T08:27:39.736596",
+ "start_time": "2020-03-30T19:54:09.085107",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.021021,
- "end_time": "2020-03-30T08:27:40.266638",
+ "duration": 0.017628,
+ "end_time": "2020-03-30T19:54:10.013048",
"exception": false,
- "start_time": "2020-03-30T08:27:40.245617",
+ "start_time": "2020-03-30T19:54:09.995420",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.021844,
- "end_time": "2020-03-30T08:27:40.297532",
+ "duration": 0.018745,
+ "end_time": "2020-03-30T19:54:10.038251",
"exception": false,
- "start_time": "2020-03-30T08:27:40.275688",
+ "start_time": "2020-03-30T19:54:10.019506",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/d1j8kx27/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/hjxho1bm/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": 0.00787,
- "end_time": "2020-03-30T08:27:40.314046",
+ "duration": 0.009672,
+ "end_time": "2020-03-30T19:54:10.055815",
"exception": false,
- "start_time": "2020-03-30T08:27:40.306176",
+ "start_time": "2020-03-30T19:54:10.046143",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.203713,
- "end_time": "2020-03-30T08:27:40.523793",
+ "duration": 0.273596,
+ "end_time": "2020-03-30T19:54:10.335256",
"exception": false,
- "start_time": "2020-03-30T08:27:40.320080",
+ "start_time": "2020-03-30T19:54:10.061660",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.027624,
- "end_time": "2020-03-30T08:27:40.565900",
+ "duration": 0.029596,
+ "end_time": "2020-03-30T19:54:10.380145",
"exception": false,
- "start_time": "2020-03-30T08:27:40.538276",
+ "start_time": "2020-03-30T19:54:10.350549",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.06934,
- "end_time": "2020-03-30T08:27:40.645200",
+ "duration": 0.07619,
+ "end_time": "2020-03-30T19:54:10.471394",
"exception": false,
- "start_time": "2020-03-30T08:27:40.575860",
+ "start_time": "2020-03-30T19:54:10.395204",
"status": "completed"
},
"tags": []
@@ -246,10 +246,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008708,
- "end_time": "2020-03-30T08:27:40.669585",
+ "duration": 0.008022,
+ "end_time": "2020-03-30T19:54:10.492176",
"exception": false,
- "start_time": "2020-03-30T08:27:40.660877",
+ "start_time": "2020-03-30T19:54:10.484154",
"status": "completed"
},
"tags": []
@@ -263,10 +263,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.189596,
- "end_time": "2020-03-30T08:27:40.865837",
+ "duration": 0.344233,
+ "end_time": "2020-03-30T19:54:10.842942",
"exception": false,
- "start_time": "2020-03-30T08:27:40.676241",
+ "start_time": "2020-03-30T19:54:10.498709",
"status": "completed"
},
"tags": []
@@ -283,10 +283,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.028367,
- "end_time": "2020-03-30T08:27:40.910685",
+ "duration": 0.029138,
+ "end_time": "2020-03-30T19:54:10.887021",
"exception": false,
- "start_time": "2020-03-30T08:27:40.882318",
+ "start_time": "2020-03-30T19:54:10.857883",
"status": "completed"
},
"tags": []
@@ -305,10 +305,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.077961,
- "end_time": "2020-03-30T08:27:40.998256",
+ "duration": 0.086462,
+ "end_time": "2020-03-30T19:54:10.983913",
"exception": false,
- "start_time": "2020-03-30T08:27:40.920295",
+ "start_time": "2020-03-30T19:54:10.897451",
"status": "completed"
},
"tags": []
@@ -455,18 +455,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 2.53769,
- "end_time": "2020-03-30T08:27:41.335247",
+ "duration": 3.267562,
+ "end_time": "2020-03-30T19:54:11.409079",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/d1j8kx27/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/hjxho1bm/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/d1j8kx27/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/hjxho1bm/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-03-30T08:27:38.797557",
+ "start_time": "2020-03-30T19:54:08.141517",
"version": "1.1.0"
}
},
--
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