From ccf4e3ca646184a3270d5f895c39445541e0f589 Mon Sep 17 00:00:00 2001
From: Chandrasekhar Ramakrishnan <cramakri@ethz.ch>
Date: Tue, 17 Mar 2020 10:09:13 +0000
Subject: [PATCH] renku update --with-siblings
---
.../46450019d71546178b97f800f3192df9.cwl | 127 +++++++++++++
data/geodata/geo_data.csv | 3 +
runs/CompileGeoData.run.ipynb | 174 ++++++++++--------
runs/Dashboard.run.ipynb | 168 ++++++++---------
4 files changed, 310 insertions(+), 162 deletions(-)
create mode 100644 .renku/workflow/46450019d71546178b97f800f3192df9.cwl
create mode 100644 data/geodata/geo_data.csv
diff --git a/.renku/workflow/46450019d71546178b97f800f3192df9.cwl b/.renku/workflow/46450019d71546178b97f800f3192df9.cwl
new file mode 100644
index 000000000..0024c42a0
--- /dev/null
+++ b/.renku/workflow/46450019d71546178b97f800f3192df9.cwl
@@ -0,0 +1,127 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: ts_folder
+ streamable: false
+ type: string
+ input_10:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/covid-19_jhu-csse
+ streamable: false
+ type: Directory
+ input_11:
+ default: rates_folder
+ streamable: false
+ type: string
+ input_12:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/covid-19_rates
+ streamable: false
+ type: Directory
+ input_13:
+ default: geodata_path
+ streamable: false
+ type: string
+ input_14:
+ default:
+ class: File
+ path: ../../data/geodata/geo_data.csv
+ streamable: false
+ type: File
+ input_15:
+ default:
+ class: File
+ path: ../../notebooks/Dashboard.ipynb
+ streamable: false
+ type: File
+ input_16:
+ default: runs/Dashboard.run.ipynb
+ streamable: false
+ type: string
+ input_2:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/covid-19_jhu-csse
+ streamable: false
+ type: Directory
+ input_3:
+ default: worldmap_path
+ streamable: false
+ type: string
+ input_4:
+ default:
+ class: File
+ path: ../../data/worldmap/country_centroids.csv
+ streamable: false
+ type: File
+ input_5:
+ default: out_folder
+ streamable: false
+ type: string
+ input_6:
+ default: data/geodata
+ streamable: false
+ type: string
+ input_7:
+ default:
+ class: File
+ path: ../../notebooks/CompileGeoData.ipynb
+ streamable: false
+ type: File
+ input_8:
+ default: runs/CompileGeoData.run.ipynb
+ streamable: false
+ type: string
+ input_9:
+ default: ts_folder
+ streamable: false
+ type: string
+outputs:
+ output_0:
+ outputSource: step_2/output_0
+ streamable: false
+ type: File
+ output_1:
+ outputSource: step_1/output_0
+ streamable: false
+ type: File
+ output_2:
+ 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
+ input_5: input_5
+ input_6: input_6
+ input_7: input_7
+ input_8: input_8
+ out:
+ - output_1
+ - output_0
+ run: 73781f74e51d4e54bc522007a2030ec2_papermill.cwl
+ step_2:
+ in:
+ input_1: input_9
+ input_2: input_10
+ input_3: input_11
+ input_4: input_12
+ input_5: input_13
+ input_6: input_14
+ input_7: input_15
+ input_8: input_16
+ out:
+ - output_0
+ run: 4cc7ffe9d5a045efb048ef2222a40ffa_papermill.cwl
diff --git a/data/geodata/geo_data.csv b/data/geodata/geo_data.csv
new file mode 100644
index 000000000..37d63a788
--- /dev/null
+++ b/data/geodata/geo_data.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:10381a7c8b37736eb65cf9c510c8a3fb3cdbd11b3c3c7a53f5a1d5a9e8e5074a
+size 34026
diff --git a/runs/CompileGeoData.run.ipynb b/runs/CompileGeoData.run.ipynb
index ed0837b40..aad5e38fd 100644
--- a/runs/CompileGeoData.run.ipynb
+++ b/runs/CompileGeoData.run.ipynb
@@ -4,10 +4,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.021165,
- "end_time": "2020-03-16T19:41:41.269273",
+ "duration": 0.022249,
+ "end_time": "2020-03-17T10:09:07.647548",
"exception": false,
- "start_time": "2020-03-16T19:41:41.248108",
+ "start_time": "2020-03-17T10:09:07.625299",
"status": "completed"
},
"tags": []
@@ -23,10 +23,10 @@
"execution_count": 1,
"metadata": {
"papermill": {
- "duration": 0.283727,
- "end_time": "2020-03-16T19:41:41.563021",
+ "duration": 0.378966,
+ "end_time": "2020-03-17T10:09:08.037220",
"exception": false,
- "start_time": "2020-03-16T19:41:41.279294",
+ "start_time": "2020-03-17T10:09:07.658254",
"status": "completed"
},
"tags": []
@@ -42,10 +42,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.024974,
- "end_time": "2020-03-16T19:41:41.606737",
+ "duration": 0.021222,
+ "end_time": "2020-03-17T10:09:08.076492",
"exception": false,
- "start_time": "2020-03-16T19:41:41.581763",
+ "start_time": "2020-03-17T10:09:08.055270",
"status": "completed"
},
"tags": []
@@ -62,10 +62,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008508,
- "end_time": "2020-03-16T19:41:41.625473",
+ "duration": 0.008239,
+ "end_time": "2020-03-17T10:09:08.093667",
"exception": false,
- "start_time": "2020-03-16T19:41:41.616965",
+ "start_time": "2020-03-17T10:09:08.085428",
"status": "completed"
},
"tags": [
@@ -81,10 +81,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.02138,
- "end_time": "2020-03-16T19:41:41.653962",
+ "duration": 0.02409,
+ "end_time": "2020-03-17T10:09:08.124799",
"exception": false,
- "start_time": "2020-03-16T19:41:41.632582",
+ "start_time": "2020-03-17T10:09:08.100709",
"status": "completed"
},
"tags": [
@@ -94,10 +94,10 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/q9ufv19r/notebooks/CompileGeoData.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/9d0h4tlx/notebooks/CompileGeoData.ipynb\"\n",
"PAPERMILL_OUTPUT_PATH = \"runs/CompileGeoData.run.ipynb\"\n",
- "ts_folder = \"/tmp/q9ufv19r/data/covid-19_jhu-csse\"\n",
- "worldmap_path = \"/tmp/q9ufv19r/data/worldmap/country_centroids.csv\"\n",
+ "ts_folder = \"/tmp/9d0h4tlx/data/covid-19_jhu-csse\"\n",
+ "worldmap_path = \"/tmp/9d0h4tlx/data/worldmap/country_centroids.csv\"\n",
"out_folder = \"data/geodata\"\n"
]
},
@@ -106,10 +106,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.025944,
- "end_time": "2020-03-16T19:41:41.689098",
+ "duration": 0.027104,
+ "end_time": "2020-03-17T10:09:08.168406",
"exception": false,
- "start_time": "2020-03-16T19:41:41.663154",
+ "start_time": "2020-03-17T10:09:08.141302",
"status": "completed"
},
"tags": []
@@ -130,10 +130,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.058376,
- "end_time": "2020-03-16T19:41:41.758318",
+ "duration": 0.0591,
+ "end_time": "2020-03-17T10:09:08.238956",
"exception": false,
- "start_time": "2020-03-16T19:41:41.699942",
+ "start_time": "2020-03-17T10:09:08.179856",
"status": "completed"
},
"tags": []
@@ -147,10 +147,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.010532,
- "end_time": "2020-03-16T19:41:41.785637",
+ "duration": 0.010019,
+ "end_time": "2020-03-17T10:09:08.263998",
"exception": false,
- "start_time": "2020-03-16T19:41:41.775105",
+ "start_time": "2020-03-17T10:09:08.253979",
"status": "completed"
},
"tags": []
@@ -164,10 +164,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.071813,
- "end_time": "2020-03-16T19:41:41.868125",
+ "duration": 0.047618,
+ "end_time": "2020-03-17T10:09:08.319197",
"exception": false,
- "start_time": "2020-03-16T19:41:41.796312",
+ "start_time": "2020-03-17T10:09:08.271579",
"status": "completed"
},
"tags": []
@@ -184,10 +184,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.043949,
- "end_time": "2020-03-16T19:41:41.931586",
+ "duration": 0.035439,
+ "end_time": "2020-03-17T10:09:08.368648",
"exception": false,
- "start_time": "2020-03-16T19:41:41.887637",
+ "start_time": "2020-03-17T10:09:08.333209",
"status": "completed"
},
"tags": []
@@ -214,10 +214,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008107,
- "end_time": "2020-03-16T19:41:41.952766",
+ "duration": 0.007979,
+ "end_time": "2020-03-17T10:09:08.387999",
"exception": false,
- "start_time": "2020-03-16T19:41:41.944659",
+ "start_time": "2020-03-17T10:09:08.380020",
"status": "completed"
},
"tags": []
@@ -231,10 +231,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.028654,
- "end_time": "2020-03-16T19:41:41.989067",
+ "duration": 0.026191,
+ "end_time": "2020-03-17T10:09:08.421750",
"exception": false,
- "start_time": "2020-03-16T19:41:41.960413",
+ "start_time": "2020-03-17T10:09:08.395559",
"status": "completed"
},
"tags": []
@@ -260,10 +260,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.021395,
- "end_time": "2020-03-16T19:41:42.022612",
+ "duration": 0.019254,
+ "end_time": "2020-03-17T10:09:08.453053",
"exception": false,
- "start_time": "2020-03-16T19:41:42.001217",
+ "start_time": "2020-03-17T10:09:08.433799",
"status": "completed"
},
"tags": []
@@ -278,10 +278,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008796,
- "end_time": "2020-03-16T19:41:42.040797",
+ "duration": 0.0076,
+ "end_time": "2020-03-17T10:09:08.470246",
"exception": false,
- "start_time": "2020-03-16T19:41:42.032001",
+ "start_time": "2020-03-17T10:09:08.462646",
"status": "completed"
},
"tags": []
@@ -295,10 +295,10 @@
"execution_count": 10,
"metadata": {
"papermill": {
- "duration": 0.044041,
- "end_time": "2020-03-16T19:41:42.092451",
+ "duration": 0.044332,
+ "end_time": "2020-03-17T10:09:08.521943",
"exception": false,
- "start_time": "2020-03-16T19:41:42.048410",
+ "start_time": "2020-03-17T10:09:08.477611",
"status": "completed"
},
"tags": []
@@ -325,8 +325,8 @@
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
- " <th>2020-03-14</th>\n",
" <th>2020-03-15</th>\n",
+ " <th>2020-03-16</th>\n",
" </tr>\n",
" <tr>\n",
" <th>Country/Region</th>\n",
@@ -337,7 +337,7 @@
" <tbody>\n",
" <tr>\n",
" <th>Congo (Brazzaville)</th>\n",
- " <td>0</td>\n",
+ " <td>1</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
@@ -351,19 +351,19 @@
" <td>696</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>Curacao</th>\n",
+ " <th>Eswatini</th>\n",
" <td>1</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>Eswatini</th>\n",
- " <td>1</td>\n",
- " <td>1</td>\n",
+ " <th>French Guiana</th>\n",
+ " <td>0</td>\n",
+ " <td>11</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Guadeloupe</th>\n",
- " <td>1</td>\n",
" <td>3</td>\n",
+ " <td>6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Holy See</th>\n",
@@ -373,17 +373,32 @@
" <tr>\n",
" <th>Martinique</th>\n",
" <td>9</td>\n",
- " <td>9</td>\n",
+ " <td>15</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Mayotte</th>\n",
+ " <td>0</td>\n",
+ " <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>North Macedonia</th>\n",
" <td>14</td>\n",
- " <td>14</td>\n",
+ " <td>18</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Republic of the Congo</th>\n",
+ " <td>0</td>\n",
+ " <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Reunion</th>\n",
- " <td>6</td>\n",
" <td>7</td>\n",
+ " <td>9</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>The Bahamas</th>\n",
+ " <td>0</td>\n",
+ " <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>occupied Palestinian territory</th>\n",
@@ -395,18 +410,21 @@
"</div>"
],
"text/plain": [
- " 2020-03-14 2020-03-15\n",
+ " 2020-03-15 2020-03-16\n",
"Country/Region \n",
- "Congo (Brazzaville) 0 1\n",
+ "Congo (Brazzaville) 1 1\n",
"Congo (Kinshasa) 2 2\n",
"Cruise Ship 696 696\n",
- "Curacao 1 1\n",
"Eswatini 1 1\n",
- "Guadeloupe 1 3\n",
+ "French Guiana 0 11\n",
+ "Guadeloupe 3 6\n",
"Holy See 1 1\n",
- "Martinique 9 9\n",
- "North Macedonia 14 14\n",
- "Reunion 6 7\n",
+ "Martinique 9 15\n",
+ "Mayotte 0 1\n",
+ "North Macedonia 14 18\n",
+ "Republic of the Congo 0 1\n",
+ "Reunion 7 9\n",
+ "The Bahamas 0 1\n",
"occupied Palestinian territory 0 0"
]
},
@@ -425,10 +443,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.009916,
- "end_time": "2020-03-16T19:41:42.118533",
+ "duration": 0.009942,
+ "end_time": "2020-03-17T10:09:08.549521",
"exception": false,
- "start_time": "2020-03-16T19:41:42.108617",
+ "start_time": "2020-03-17T10:09:08.539579",
"status": "completed"
},
"tags": []
@@ -442,10 +460,10 @@
"execution_count": 11,
"metadata": {
"papermill": {
- "duration": 0.033068,
- "end_time": "2020-03-16T19:41:42.159802",
+ "duration": 0.031984,
+ "end_time": "2020-03-17T10:09:08.589686",
"exception": false,
- "start_time": "2020-03-16T19:41:42.126734",
+ "start_time": "2020-03-17T10:09:08.557702",
"status": "completed"
},
"tags": []
@@ -477,20 +495,20 @@
"version": "3.7.6"
},
"papermill": {
- "duration": 1.96386,
- "end_time": "2020-03-16T19:41:42.484999",
+ "duration": 2.13034,
+ "end_time": "2020-03-17T10:09:08.914717",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/q9ufv19r/notebooks/CompileGeoData.ipynb",
+ "input_path": "/tmp/9d0h4tlx/notebooks/CompileGeoData.ipynb",
"output_path": "runs/CompileGeoData.run.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/q9ufv19r/notebooks/CompileGeoData.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/9d0h4tlx/notebooks/CompileGeoData.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/CompileGeoData.run.ipynb",
"out_folder": "data/geodata",
- "ts_folder": "/tmp/q9ufv19r/data/covid-19_jhu-csse",
- "worldmap_path": "/tmp/q9ufv19r/data/worldmap/country_centroids.csv"
+ "ts_folder": "/tmp/9d0h4tlx/data/covid-19_jhu-csse",
+ "worldmap_path": "/tmp/9d0h4tlx/data/worldmap/country_centroids.csv"
},
- "start_time": "2020-03-16T19:41:40.521139",
+ "start_time": "2020-03-17T10:09:06.784377",
"version": "1.1.0"
}
},
diff --git a/runs/Dashboard.run.ipynb b/runs/Dashboard.run.ipynb
index ced6bac53..b460da6c2 100644
--- a/runs/Dashboard.run.ipynb
+++ b/runs/Dashboard.run.ipynb
@@ -5,10 +5,10 @@
"execution_count": 1,
"metadata": {
"papermill": {
- "duration": 0.451143,
- "end_time": "2020-03-16T19:51:54.290899",
+ "duration": 0.469742,
+ "end_time": "2020-03-17T10:09:11.101438",
"exception": false,
- "start_time": "2020-03-16T19:51:53.839756",
+ "start_time": "2020-03-17T10:09:10.631696",
"status": "completed"
},
"tags": []
@@ -27,10 +27,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.023102,
- "end_time": "2020-03-16T19:51:54.333675",
+ "duration": 0.03326,
+ "end_time": "2020-03-17T10:09:11.157505",
"exception": false,
- "start_time": "2020-03-16T19:51:54.310573",
+ "start_time": "2020-03-17T10:09:11.124245",
"status": "completed"
},
"tags": [
@@ -51,10 +51,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.02233,
- "end_time": "2020-03-16T19:51:54.366926",
+ "duration": 0.024282,
+ "end_time": "2020-03-17T10:09:11.200233",
"exception": false,
- "start_time": "2020-03-16T19:51:54.344596",
+ "start_time": "2020-03-17T10:09:11.175951",
"status": "completed"
},
"tags": [
@@ -64,11 +64,11 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/ua0ak07f/notebooks/Dashboard.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/nun9h85i/notebooks/Dashboard.ipynb\"\n",
"PAPERMILL_OUTPUT_PATH = \"runs/Dashboard.run.ipynb\"\n",
- "ts_folder = \"/tmp/ua0ak07f/data/covid-19_jhu-csse\"\n",
- "rates_folder = \"/tmp/ua0ak07f/data/covid-19_rates\"\n",
- "geodata_path = \"/tmp/ua0ak07f/data/geodata/geo_data.csv\"\n"
+ "ts_folder = \"/tmp/nun9h85i/data/covid-19_jhu-csse\"\n",
+ "rates_folder = \"/tmp/nun9h85i/data/covid-19_rates\"\n",
+ "geodata_path = \"/tmp/nun9h85i/data/geodata/geo_data.csv\"\n"
]
},
{
@@ -76,10 +76,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.020859,
- "end_time": "2020-03-16T19:51:54.398133",
+ "duration": 0.02124,
+ "end_time": "2020-03-17T10:09:11.234670",
"exception": false,
- "start_time": "2020-03-16T19:51:54.377274",
+ "start_time": "2020-03-17T10:09:11.213430",
"status": "completed"
},
"tags": []
@@ -94,10 +94,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.114706,
- "end_time": "2020-03-16T19:51:54.522622",
+ "duration": 0.120931,
+ "end_time": "2020-03-17T10:09:11.366355",
"exception": false,
- "start_time": "2020-03-16T19:51:54.407916",
+ "start_time": "2020-03-17T10:09:11.245424",
"status": "completed"
},
"tags": []
@@ -118,10 +118,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
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@@ -323,10 +323,10 @@
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"metadata": {
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@@ -439,10 +439,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.012164,
- "end_time": "2020-03-16T19:51:55.015521",
+ "duration": 0.011818,
+ "end_time": "2020-03-17T10:09:11.825949",
"exception": false,
- "start_time": "2020-03-16T19:51:55.003357",
+ "start_time": "2020-03-17T10:09:11.814131",
"status": "completed"
},
"tags": []
@@ -456,10 +456,10 @@
"execution_count": 11,
"metadata": {
"papermill": {
- "duration": 0.068477,
- "end_time": "2020-03-16T19:51:55.096657",
+ "duration": 0.063665,
+ "end_time": "2020-03-17T10:09:11.900709",
"exception": false,
- "start_time": "2020-03-16T19:51:55.028180",
+ "start_time": "2020-03-17T10:09:11.837044",
"status": "completed"
},
"tags": []
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"</script>"
],
"text/plain": [
@@ -912,20 +912,20 @@
"version": "3.7.6"
},
"papermill": {
- "duration": 3.426033,
- "end_time": "2020-03-16T19:51:56.424491",
+ "duration": 3.509676,
+ "end_time": "2020-03-17T10:09:13.296121",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/ua0ak07f/notebooks/Dashboard.ipynb",
+ "input_path": "/tmp/nun9h85i/notebooks/Dashboard.ipynb",
"output_path": "runs/Dashboard.run.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/ua0ak07f/notebooks/Dashboard.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/nun9h85i/notebooks/Dashboard.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/Dashboard.run.ipynb",
- "geodata_path": "/tmp/ua0ak07f/data/geodata/geo_data.csv",
- "rates_folder": "/tmp/ua0ak07f/data/covid-19_rates",
- "ts_folder": "/tmp/ua0ak07f/data/covid-19_jhu-csse"
+ "geodata_path": "/tmp/nun9h85i/data/geodata/geo_data.csv",
+ "rates_folder": "/tmp/nun9h85i/data/covid-19_rates",
+ "ts_folder": "/tmp/nun9h85i/data/covid-19_jhu-csse"
},
- "start_time": "2020-03-16T19:51:52.998458",
+ "start_time": "2020-03-17T10:09:09.786445",
"version": "1.1.0"
}
},
--
GitLab