From 2448967fa12dcff17c565683bbd88d369e2dd0a4 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <cramakri+covid-cron@ethz.ch>
Date: Thu, 30 Apr 2020 20:39:38 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../bf45cb4d1740458e971c5c555d51e3ae.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/bf45cb4d1740458e971c5c555d51e3ae.cwl
diff --git a/.renku/workflow/bf45cb4d1740458e971c5c555d51e3ae.cwl b/.renku/workflow/bf45cb4d1740458e971c5c555d51e3ae.cwl
new file mode 100644
index 000000000..6912aafa9
--- /dev/null
+++ b/.renku/workflow/bf45cb4d1740458e971c5c555d51e3ae.cwl
@@ -0,0 +1,148 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: out_folder
+ streamable: false
+ type: string
+ input_10:
+ default: states-metadata.json
+ streamable: false
+ type: string
+ input_2:
+ default: data/covidtracking
+ streamable: false
+ type: string
+ input_3:
+ default:
+ class: File
+ path: ../../notebooks/process/download-covidtracking-data.ipynb
+ streamable: false
+ type: File
+ input_4:
+ default: runs/download-covidtracking-data.runs.ipynb
+ streamable: false
+ type: string
+ input_5:
+ default: states-daily.json
+ 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_1:
+ outputSource: step_1/output_0
+ streamable: false
+ type: File
+ output_3:
+ outputSource: step_1/output_1
+ streamable: false
+ type: Directory
+requirements: []
+steps:
+ step_1:
+ in:
+ input_1: input_1
+ input_2: input_2
+ input_3: input_3
+ input_4: input_4
+ out:
+ - output_0
+ - output_1
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
+ step_2:
+ in:
+ filename: input_5
+ 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_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_1/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 1b830ed4e..e4ede11ba 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:b1aee7944a94451ab257145cd55497c11f26841b6071f5854817ad8d41d46576
-size 1530498
+oid sha256:de4b330e16d1440786340b4751e413d340c791f2ff303ed6ef576cb036f10a2f
+size 1562090
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index db5f4e07a..bfddaa037 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 sha256:1e5e886f27600015ae7ecab4c43995eb043c8370a0c8d6c26e4f9bffad486693
-size 30080
+oid sha256:3d5c8aaa3c2c56321df18cd2f9e3d851a1948cef43863db7f9213010a6dbc72a
+size 29992
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index d943a81fe..3e46874d4 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": 3.865322,
- "end_time": "2020-04-29T07:27:05.870354",
+ "duration": 0.485688,
+ "end_time": "2020-04-30T20:39:31.475755",
"exception": false,
- "start_time": "2020-04-29T07:27:02.005032",
+ "start_time": "2020-04-30T20:39:30.990067",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.021783,
- "end_time": "2020-04-29T07:27:05.905512",
+ "duration": 0.022523,
+ "end_time": "2020-04-30T20:39:31.508540",
"exception": false,
- "start_time": "2020-04-29T07:27:05.883729",
+ "start_time": "2020-04-30T20:39:31.486017",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.027562,
- "end_time": "2020-04-29T07:27:05.941731",
+ "duration": 0.023961,
+ "end_time": "2020-04-30T20:39:31.546006",
"exception": false,
- "start_time": "2020-04-29T07:27:05.914169",
+ "start_time": "2020-04-30T20:39:31.522045",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/1dxcr_ip/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/q32lk3hk/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": 0.008265,
- "end_time": "2020-04-29T07:27:05.964251",
+ "duration": 0.005595,
+ "end_time": "2020-04-30T20:39:31.559832",
"exception": false,
- "start_time": "2020-04-29T07:27:05.955986",
+ "start_time": "2020-04-30T20:39:31.554237",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.580459,
- "end_time": "2020-04-29T07:27:06.551574",
+ "duration": 2.797905,
+ "end_time": "2020-04-30T20:39:34.363335",
"exception": false,
- "start_time": "2020-04-29T07:27:05.971115",
+ "start_time": "2020-04-30T20:39:31.565430",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.028027,
- "end_time": "2020-04-29T07:27:06.597151",
+ "duration": 0.028778,
+ "end_time": "2020-04-30T20:39:34.408538",
"exception": false,
- "start_time": "2020-04-29T07:27:06.569124",
+ "start_time": "2020-04-30T20:39:34.379760",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.074928,
- "end_time": "2020-04-29T07:27:06.682377",
+ "duration": 0.072536,
+ "end_time": "2020-04-30T20:39:34.493093",
"exception": false,
- "start_time": "2020-04-29T07:27:06.607449",
+ "start_time": "2020-04-30T20:39:34.420557",
"status": "completed"
},
"tags": []
@@ -246,10 +246,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007555,
- "end_time": "2020-04-29T07:27:06.701924",
+ "duration": 0.007706,
+ "end_time": "2020-04-30T20:39:34.515266",
"exception": false,
- "start_time": "2020-04-29T07:27:06.694369",
+ "start_time": "2020-04-30T20:39:34.507560",
"status": "completed"
},
"tags": []
@@ -263,10 +263,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.308747,
- "end_time": "2020-04-29T07:27:07.017018",
+ "duration": 0.12028,
+ "end_time": "2020-04-30T20:39:34.642136",
"exception": false,
- "start_time": "2020-04-29T07:27:06.708271",
+ "start_time": "2020-04-30T20:39:34.521856",
"status": "completed"
},
"tags": []
@@ -283,10 +283,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.031866,
- "end_time": "2020-04-29T07:27:07.065408",
+ "duration": 0.031997,
+ "end_time": "2020-04-30T20:39:34.688913",
"exception": false,
- "start_time": "2020-04-29T07:27:07.033542",
+ "start_time": "2020-04-30T20:39:34.656916",
"status": "completed"
},
"tags": []
@@ -305,10 +305,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.118292,
- "end_time": "2020-04-29T07:27:07.194849",
+ "duration": 0.11394,
+ "end_time": "2020-04-30T20:39:34.814486",
"exception": false,
- "start_time": "2020-04-29T07:27:07.076557",
+ "start_time": "2020-04-30T20:39:34.700546",
"status": "completed"
},
"tags": []
@@ -318,7 +318,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "3041 data points\n"
+ "3097 data points\n"
]
},
{
@@ -368,51 +368,51 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200428</td>\n",
+ " <td>20200429</td>\n",
" <td>AK</td>\n",
- " <td>351.0</td>\n",
- " <td>16738.0</td>\n",
+ " <td>355.0</td>\n",
+ " <td>18764.0</td>\n",
" <td>NaN</td>\n",
- " <td>16.0</td>\n",
+ " <td>14.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
" <td>NaN</td>\n",
- " <td>17089.0</td>\n",
- " <td>17089.0</td>\n",
- " <td>17089.0</td>\n",
+ " <td>19119.0</td>\n",
+ " <td>19119.0</td>\n",
+ " <td>19119.0</td>\n",
" <td>2</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
- " <td>827.0</td>\n",
- " <td>6.0</td>\n",
- " <td>833.0</td>\n",
+ " <td>2026.0</td>\n",
+ " <td>4.0</td>\n",
+ " <td>2030.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200428</td>\n",
+ " <td>20200429</td>\n",
" <td>AL</td>\n",
- " <td>6687.0</td>\n",
- " <td>69140.0</td>\n",
+ " <td>6842.0</td>\n",
+ " <td>73607.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>911.0</td>\n",
+ " <td>945.0</td>\n",
" <td>NaN</td>\n",
" <td>335.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>911.0</td>\n",
- " <td>75827.0</td>\n",
- " <td>75827.0</td>\n",
- " <td>75827.0</td>\n",
+ " <td>945.0</td>\n",
+ " <td>80449.0</td>\n",
+ " <td>80449.0</td>\n",
+ " <td>80449.0</td>\n",
" <td>1</td>\n",
- " <td>20.0</td>\n",
- " <td>39.0</td>\n",
- " <td>1642.0</td>\n",
- " <td>188.0</td>\n",
- " <td>1830.0</td>\n",
+ " <td>3.0</td>\n",
+ " <td>34.0</td>\n",
+ " <td>4467.0</td>\n",
+ " <td>155.0</td>\n",
+ " <td>4622.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
@@ -421,24 +421,24 @@
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200428 AK 351.0 16738.0 NaN 16.0 \n",
- "1 20200428 AL 6687.0 69140.0 NaN NaN \n",
+ "0 20200429 AK 355.0 18764.0 NaN 14.0 \n",
+ "1 20200429 AL 6842.0 73607.0 NaN NaN \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 911.0 NaN 335.0 \n",
+ "1 945.0 NaN 335.0 \n",
"\n",
" onVentilatorCurrently ... hospitalized total totalTestResults \\\n",
- "0 NaN ... NaN 17089.0 17089.0 \n",
- "1 NaN ... 911.0 75827.0 75827.0 \n",
+ "0 NaN ... NaN 19119.0 19119.0 \n",
+ "1 NaN ... 945.0 80449.0 80449.0 \n",
"\n",
" posNeg fips deathIncrease hospitalizedIncrease negativeIncrease \\\n",
- "0 17089.0 2 0.0 0.0 827.0 \n",
- "1 75827.0 1 20.0 39.0 1642.0 \n",
+ "0 19119.0 2 0.0 0.0 2026.0 \n",
+ "1 80449.0 1 3.0 34.0 4467.0 \n",
"\n",
" positiveIncrease totalTestResultsIncrease \n",
- "0 6.0 833.0 \n",
- "1 188.0 1830.0 \n",
+ "0 4.0 2030.0 \n",
+ "1 155.0 4622.0 \n",
"\n",
"[2 rows x 25 columns]"
]
@@ -474,18 +474,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 7.505897,
- "end_time": "2020-04-29T07:27:07.518570",
+ "duration": 5.073446,
+ "end_time": "2020-04-30T20:39:35.130808",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/1dxcr_ip/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/q32lk3hk/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/1dxcr_ip/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/q32lk3hk/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-04-29T07:27:00.012673",
+ "start_time": "2020-04-30T20:39:30.057362",
"version": "1.1.0"
}
},
--
GitLab