From 638d6c01ebddcfa0b23d02fbbb2b25c02e021883 Mon Sep 17 00:00:00 2001
From: Chandrasekhar Ramakrishnan <cramakri@ethz.ch>
Date: Wed, 18 Mar 2020 17:39:47 +0000
Subject: [PATCH] renku run papermill -p ts_folder ./data/covid-19_jhu-csse/ -p
worldmap_path ./data/worldmap/country_centroids.csv -p out_folder
./data/geodata/ --inject-paths notebooks/process/CompileGeoData.ipynb
runs/CompileGeoData.run.ipynb
---
...f47629164158a118963ae58eea3b_papermill.cwl | 113 ++++++++++++++++
runs/CompileGeoData.run.ipynb | 126 +++++++++---------
2 files changed, 176 insertions(+), 63 deletions(-)
create mode 100644 .renku/workflow/a8b2f47629164158a118963ae58eea3b_papermill.cwl
diff --git a/.renku/workflow/a8b2f47629164158a118963ae58eea3b_papermill.cwl b/.renku/workflow/a8b2f47629164158a118963ae58eea3b_papermill.cwl
new file mode 100644
index 00000000..c44a8022
--- /dev/null
+++ b/.renku/workflow/a8b2f47629164158a118963ae58eea3b_papermill.cwl
@@ -0,0 +1,113 @@
+arguments: []
+baseCommand:
+- papermill
+class: CommandLineTool
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: ts_folder
+ inputBinding:
+ position: 1
+ prefix: -p
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_2:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/covid-19_jhu-csse
+ inputBinding:
+ position: 2
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: Directory
+ input_3:
+ default: worldmap_path
+ inputBinding:
+ position: 3
+ prefix: -p
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_4:
+ default:
+ class: File
+ path: ../../data/worldmap/country_centroids.csv
+ inputBinding:
+ position: 4
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: File
+ input_5:
+ default: out_folder
+ inputBinding:
+ position: 5
+ prefix: -p
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_6:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/geodata
+ inputBinding:
+ position: 6
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: Directory
+ input_7:
+ default:
+ class: File
+ path: ../../notebooks/process/CompileGeoData.ipynb
+ inputBinding:
+ position: 7
+ prefix: --inject-paths
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: File
+ input_8:
+ default: runs/CompileGeoData.run.ipynb
+ inputBinding:
+ position: 8
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+outputs:
+ output_0:
+ outputBinding:
+ glob: $(inputs.input_8)
+ streamable: false
+ type: File
+permanentFailCodes: []
+requirements:
+- class: InlineJavascriptRequirement
+- class: InitialWorkDirRequirement
+ listing:
+ - entry: '$({"listing": [], "class": "Directory"})'
+ entryname: runs
+ writable: true
+ - entry: $(inputs.input_2)
+ entryname: data/covid-19_jhu-csse
+ writable: false
+ - entry: $(inputs.input_4)
+ entryname: data/worldmap/country_centroids.csv
+ writable: false
+ - entry: $(inputs.input_6)
+ entryname: data/geodata
+ writable: false
+ - entry: $(inputs.input_7)
+ entryname: notebooks/process/CompileGeoData.ipynb
+ writable: false
+successCodes: []
+temporaryFailCodes: []
diff --git a/runs/CompileGeoData.run.ipynb b/runs/CompileGeoData.run.ipynb
index f9bd0e20..a19c4069 100644
--- a/runs/CompileGeoData.run.ipynb
+++ b/runs/CompileGeoData.run.ipynb
@@ -4,10 +4,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.016474,
- "end_time": "2020-03-18T17:20:53.504777",
+ "duration": 0.019915,
+ "end_time": "2020-03-18T17:39:45.438621",
"exception": false,
- "start_time": "2020-03-18T17:20:53.488303",
+ "start_time": "2020-03-18T17:39:45.418706",
"status": "completed"
},
"tags": []
@@ -23,10 +23,10 @@
"execution_count": 1,
"metadata": {
"papermill": {
- "duration": 0.329109,
- "end_time": "2020-03-18T17:20:53.844329",
+ "duration": 0.356977,
+ "end_time": "2020-03-18T17:39:45.806137",
"exception": false,
- "start_time": "2020-03-18T17:20:53.515220",
+ "start_time": "2020-03-18T17:39:45.449160",
"status": "completed"
},
"tags": []
@@ -42,10 +42,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.018825,
- "end_time": "2020-03-18T17:20:53.878971",
+ "duration": 0.020489,
+ "end_time": "2020-03-18T17:39:45.839942",
"exception": false,
- "start_time": "2020-03-18T17:20:53.860146",
+ "start_time": "2020-03-18T17:39:45.819453",
"status": "completed"
},
"tags": []
@@ -62,10 +62,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.009852,
- "end_time": "2020-03-18T17:20:53.900179",
+ "duration": 0.010294,
+ "end_time": "2020-03-18T17:39:45.862217",
"exception": false,
- "start_time": "2020-03-18T17:20:53.890327",
+ "start_time": "2020-03-18T17:39:45.851923",
"status": "completed"
},
"tags": [
@@ -81,10 +81,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.021389,
- "end_time": "2020-03-18T17:20:53.931545",
+ "duration": 0.023154,
+ "end_time": "2020-03-18T17:39:45.909658",
"exception": false,
- "start_time": "2020-03-18T17:20:53.910156",
+ "start_time": "2020-03-18T17:39:45.886504",
"status": "completed"
},
"tags": [
@@ -94,11 +94,11 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/dixae90v/notebooks/CompileGeoData.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"notebooks/process/CompileGeoData.ipynb\"\n",
"PAPERMILL_OUTPUT_PATH = \"runs/CompileGeoData.run.ipynb\"\n",
- "ts_folder = \"/tmp/dixae90v/data/covid-19_jhu-csse\"\n",
- "worldmap_path = \"/tmp/dixae90v/data/worldmap/country_centroids.csv\"\n",
- "out_folder = \"data/geodata\"\n"
+ "ts_folder = \"./data/covid-19_jhu-csse/\"\n",
+ "worldmap_path = \"./data/worldmap/country_centroids.csv\"\n",
+ "out_folder = \"./data/geodata/\"\n"
]
},
{
@@ -106,10 +106,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.023787,
- "end_time": "2020-03-18T17:20:53.966187",
+ "duration": 0.022631,
+ "end_time": "2020-03-18T17:39:45.942649",
"exception": false,
- "start_time": "2020-03-18T17:20:53.942400",
+ "start_time": "2020-03-18T17:39:45.920018",
"status": "completed"
},
"tags": []
@@ -130,10 +130,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.054163,
- "end_time": "2020-03-18T17:20:54.033789",
+ "duration": 0.05949,
+ "end_time": "2020-03-18T17:39:46.014614",
"exception": false,
- "start_time": "2020-03-18T17:20:53.979626",
+ "start_time": "2020-03-18T17:39:45.955124",
"status": "completed"
},
"tags": []
@@ -147,10 +147,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.009594,
- "end_time": "2020-03-18T17:20:54.055575",
+ "duration": 0.010077,
+ "end_time": "2020-03-18T17:39:46.041211",
"exception": false,
- "start_time": "2020-03-18T17:20:54.045981",
+ "start_time": "2020-03-18T17:39:46.031134",
"status": "completed"
},
"tags": []
@@ -164,10 +164,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.041843,
- "end_time": "2020-03-18T17:20:54.107149",
+ "duration": 0.043439,
+ "end_time": "2020-03-18T17:39:46.094285",
"exception": false,
- "start_time": "2020-03-18T17:20:54.065306",
+ "start_time": "2020-03-18T17:39:46.050846",
"status": "completed"
},
"tags": []
@@ -184,10 +184,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.034309,
- "end_time": "2020-03-18T17:20:54.157853",
+ "duration": 0.034514,
+ "end_time": "2020-03-18T17:39:46.142439",
"exception": false,
- "start_time": "2020-03-18T17:20:54.123544",
+ "start_time": "2020-03-18T17:39:46.107925",
"status": "completed"
},
"tags": []
@@ -214,10 +214,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.009863,
- "end_time": "2020-03-18T17:20:54.181948",
+ "duration": 0.009928,
+ "end_time": "2020-03-18T17:39:46.166476",
"exception": false,
- "start_time": "2020-03-18T17:20:54.172085",
+ "start_time": "2020-03-18T17:39:46.156548",
"status": "completed"
},
"tags": []
@@ -231,10 +231,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.024119,
- "end_time": "2020-03-18T17:20:54.216240",
+ "duration": 0.026025,
+ "end_time": "2020-03-18T17:39:46.202465",
"exception": false,
- "start_time": "2020-03-18T17:20:54.192121",
+ "start_time": "2020-03-18T17:39:46.176440",
"status": "completed"
},
"tags": []
@@ -260,10 +260,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.018305,
- "end_time": "2020-03-18T17:20:54.247866",
+ "duration": 0.018618,
+ "end_time": "2020-03-18T17:39:46.232915",
"exception": false,
- "start_time": "2020-03-18T17:20:54.229561",
+ "start_time": "2020-03-18T17:39:46.214297",
"status": "completed"
},
"tags": []
@@ -278,10 +278,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.009955,
- "end_time": "2020-03-18T17:20:54.267709",
+ "duration": 0.009895,
+ "end_time": "2020-03-18T17:39:46.253760",
"exception": false,
- "start_time": "2020-03-18T17:20:54.257754",
+ "start_time": "2020-03-18T17:39:46.243865",
"status": "completed"
},
"tags": []
@@ -295,10 +295,10 @@
"execution_count": 10,
"metadata": {
"papermill": {
- "duration": 0.036233,
- "end_time": "2020-03-18T17:20:54.313980",
+ "duration": 0.034717,
+ "end_time": "2020-03-18T17:39:46.298658",
"exception": false,
- "start_time": "2020-03-18T17:20:54.277747",
+ "start_time": "2020-03-18T17:39:46.263941",
"status": "completed"
},
"tags": []
@@ -413,10 +413,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.010645,
- "end_time": "2020-03-18T17:20:54.337794",
+ "duration": 0.010396,
+ "end_time": "2020-03-18T17:39:46.322850",
"exception": false,
- "start_time": "2020-03-18T17:20:54.327149",
+ "start_time": "2020-03-18T17:39:46.312454",
"status": "completed"
},
"tags": []
@@ -430,10 +430,10 @@
"execution_count": 11,
"metadata": {
"papermill": {
- "duration": 0.031073,
- "end_time": "2020-03-18T17:20:54.379882",
+ "duration": 0.028961,
+ "end_time": "2020-03-18T17:39:46.362455",
"exception": false,
- "start_time": "2020-03-18T17:20:54.348809",
+ "start_time": "2020-03-18T17:39:46.333494",
"status": "completed"
},
"tags": []
@@ -465,20 +465,20 @@
"version": "3.7.6"
},
"papermill": {
- "duration": 2.08007,
- "end_time": "2020-03-18T17:20:54.703617",
+ "duration": 2.135836,
+ "end_time": "2020-03-18T17:39:46.683682",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/dixae90v/notebooks/CompileGeoData.ipynb",
+ "input_path": "notebooks/process/CompileGeoData.ipynb",
"output_path": "runs/CompileGeoData.run.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/dixae90v/notebooks/CompileGeoData.ipynb",
+ "PAPERMILL_INPUT_PATH": "notebooks/process/CompileGeoData.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/CompileGeoData.run.ipynb",
- "out_folder": "data/geodata",
- "ts_folder": "/tmp/dixae90v/data/covid-19_jhu-csse",
- "worldmap_path": "/tmp/dixae90v/data/worldmap/country_centroids.csv"
+ "out_folder": "./data/geodata/",
+ "ts_folder": "./data/covid-19_jhu-csse/",
+ "worldmap_path": "./data/worldmap/country_centroids.csv"
},
- "start_time": "2020-03-18T17:20:52.623547",
+ "start_time": "2020-03-18T17:39:44.547846",
"version": "1.1.0"
}
},
--
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