diff --git a/.renku/workflow/c1e3191700aa4231a584f4eb0fac4631.cwl b/.renku/workflow/c1e3191700aa4231a584f4eb0fac4631.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..0ba55fb7ade270519e21ba262860082db682746a
--- /dev/null
+++ b/.renku/workflow/c1e3191700aa4231a584f4eb0fac4631.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_1
+ streamable: false
+ type: Directory
+ output_2:
+ outputSource: step_1/output_0
+ streamable: false
+ type: File
+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_0
+ - output_1
+ 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 0000000000000000000000000000000000000000..37d63a7880e889979c94bd91b982fa1aae083863
--- /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 de20d0961e2d07b09a60e8cb3f9b379cd4f8ec35..ed0837b4041f68cf72ee3542b31c9d1fba93be27 100644
--- a/runs/CompileGeoData.run.ipynb
+++ b/runs/CompileGeoData.run.ipynb
@@ -4,10 +4,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.025663,
- "end_time": "2020-03-15T16:43:49.005977",
+ "duration": 0.021165,
+ "end_time": "2020-03-16T19:41:41.269273",
"exception": false,
- "start_time": "2020-03-15T16:43:48.980314",
+ "start_time": "2020-03-16T19:41:41.248108",
"status": "completed"
},
"tags": []
@@ -23,10 +23,10 @@
"execution_count": 1,
"metadata": {
"papermill": {
- "duration": 0.285624,
- "end_time": "2020-03-15T16:43:49.302040",
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"exception": false,
- "start_time": "2020-03-15T16:43:49.016416",
+ "start_time": "2020-03-16T19:41:41.279294",
"status": "completed"
},
"tags": []
@@ -42,10 +42,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.057379,
- "end_time": "2020-03-15T16:43:49.376597",
+ "duration": 0.024974,
+ "end_time": "2020-03-16T19:41:41.606737",
"exception": false,
- "start_time": "2020-03-15T16:43:49.319218",
+ "start_time": "2020-03-16T19:41:41.581763",
"status": "completed"
},
"tags": []
@@ -62,10 +62,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.015419,
- "end_time": "2020-03-15T16:43:49.400508",
+ "duration": 0.008508,
+ "end_time": "2020-03-16T19:41:41.625473",
"exception": false,
- "start_time": "2020-03-15T16:43:49.385089",
+ "start_time": "2020-03-16T19:41:41.616965",
"status": "completed"
},
"tags": [
@@ -81,10 +81,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.019117,
- "end_time": "2020-03-15T16:43:49.427165",
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+ "end_time": "2020-03-16T19:41:41.653962",
"exception": false,
- "start_time": "2020-03-15T16:43:49.408048",
+ "start_time": "2020-03-16T19:41:41.632582",
"status": "completed"
},
"tags": [
@@ -94,10 +94,10 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/262jiqqx/notebooks/CompileGeoData.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/q9ufv19r/notebooks/CompileGeoData.ipynb\"\n",
"PAPERMILL_OUTPUT_PATH = \"runs/CompileGeoData.run.ipynb\"\n",
- "ts_folder = \"/tmp/262jiqqx/data/covid-19_jhu-csse\"\n",
- "worldmap_path = \"/tmp/262jiqqx/data/worldmap/country_centroids.csv\"\n",
+ "ts_folder = \"/tmp/q9ufv19r/data/covid-19_jhu-csse\"\n",
+ "worldmap_path = \"/tmp/q9ufv19r/data/worldmap/country_centroids.csv\"\n",
"out_folder = \"data/geodata\"\n"
]
},
@@ -106,10 +106,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.019727,
- "end_time": "2020-03-15T16:43:49.457802",
+ "duration": 0.025944,
+ "end_time": "2020-03-16T19:41:41.689098",
"exception": false,
- "start_time": "2020-03-15T16:43:49.438075",
+ "start_time": "2020-03-16T19:41:41.663154",
"status": "completed"
},
"tags": []
@@ -130,10 +130,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.057337,
- "end_time": "2020-03-15T16:43:49.523781",
+ "duration": 0.058376,
+ "end_time": "2020-03-16T19:41:41.758318",
"exception": false,
- "start_time": "2020-03-15T16:43:49.466444",
+ "start_time": "2020-03-16T19:41:41.699942",
"status": "completed"
},
"tags": []
@@ -147,10 +147,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008192,
- "end_time": "2020-03-15T16:43:49.544325",
+ "duration": 0.010532,
+ "end_time": "2020-03-16T19:41:41.785637",
"exception": false,
- "start_time": "2020-03-15T16:43:49.536133",
+ "start_time": "2020-03-16T19:41:41.775105",
"status": "completed"
},
"tags": []
@@ -164,10 +164,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.04304,
- "end_time": "2020-03-15T16:43:49.594611",
+ "duration": 0.071813,
+ "end_time": "2020-03-16T19:41:41.868125",
"exception": false,
- "start_time": "2020-03-15T16:43:49.551571",
+ "start_time": "2020-03-16T19:41:41.796312",
"status": "completed"
},
"tags": []
@@ -184,10 +184,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.033254,
- "end_time": "2020-03-15T16:43:49.644104",
+ "duration": 0.043949,
+ "end_time": "2020-03-16T19:41:41.931586",
"exception": false,
- "start_time": "2020-03-15T16:43:49.610850",
+ "start_time": "2020-03-16T19:41:41.887637",
"status": "completed"
},
"tags": []
@@ -214,10 +214,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007079,
- "end_time": "2020-03-15T16:43:49.660788",
+ "duration": 0.008107,
+ "end_time": "2020-03-16T19:41:41.952766",
"exception": false,
- "start_time": "2020-03-15T16:43:49.653709",
+ "start_time": "2020-03-16T19:41:41.944659",
"status": "completed"
},
"tags": []
@@ -231,10 +231,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.027734,
- "end_time": "2020-03-15T16:43:49.695692",
+ "duration": 0.028654,
+ "end_time": "2020-03-16T19:41:41.989067",
"exception": false,
- "start_time": "2020-03-15T16:43:49.667958",
+ "start_time": "2020-03-16T19:41:41.960413",
"status": "completed"
},
"tags": []
@@ -260,10 +260,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.019985,
- "end_time": "2020-03-15T16:43:49.727444",
+ "duration": 0.021395,
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"exception": false,
- "start_time": "2020-03-15T16:43:49.707459",
+ "start_time": "2020-03-16T19:41:42.001217",
"status": "completed"
},
"tags": []
@@ -278,10 +278,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008364,
- "end_time": "2020-03-15T16:43:49.744328",
+ "duration": 0.008796,
+ "end_time": "2020-03-16T19:41:42.040797",
"exception": false,
- "start_time": "2020-03-15T16:43:49.735964",
+ "start_time": "2020-03-16T19:41:42.032001",
"status": "completed"
},
"tags": []
@@ -295,10 +295,10 @@
"execution_count": 10,
"metadata": {
"papermill": {
- "duration": 0.038721,
- "end_time": "2020-03-15T16:43:49.790199",
+ "duration": 0.044041,
+ "end_time": "2020-03-16T19:41:42.092451",
"exception": false,
- "start_time": "2020-03-15T16:43:49.751478",
+ "start_time": "2020-03-16T19:41:42.048410",
"status": "completed"
},
"tags": []
@@ -325,8 +325,8 @@
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
- " <th>2020-03-13</th>\n",
" <th>2020-03-14</th>\n",
+ " <th>2020-03-15</th>\n",
" </tr>\n",
" <tr>\n",
" <th>Country/Region</th>\n",
@@ -336,6 +336,11 @@
" </thead>\n",
" <tbody>\n",
" <tr>\n",
+ " <th>Congo (Brazzaville)</th>\n",
+ " <td>0</td>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
" <th>Congo (Kinshasa)</th>\n",
" <td>2</td>\n",
" <td>2</td>\n",
@@ -347,23 +352,18 @@
" </tr>\n",
" <tr>\n",
" <th>Curacao</th>\n",
- " <td>0</td>\n",
+ " <td>1</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Eswatini</th>\n",
- " <td>0</td>\n",
" <td>1</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>French Guiana</th>\n",
- " <td>5</td>\n",
- " <td>5</td>\n",
+ " <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Guadeloupe</th>\n",
" <td>1</td>\n",
- " <td>1</td>\n",
+ " <td>3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Holy See</th>\n",
@@ -372,7 +372,7 @@
" </tr>\n",
" <tr>\n",
" <th>Martinique</th>\n",
- " <td>3</td>\n",
+ " <td>9</td>\n",
" <td>9</td>\n",
" </tr>\n",
" <tr>\n",
@@ -382,8 +382,8 @@
" </tr>\n",
" <tr>\n",
" <th>Reunion</th>\n",
- " <td>5</td>\n",
" <td>6</td>\n",
+ " <td>7</td>\n",
" </tr>\n",
" <tr>\n",
" <th>occupied Palestinian territory</th>\n",
@@ -395,18 +395,18 @@
"</div>"
],
"text/plain": [
- " 2020-03-13 2020-03-14\n",
+ " 2020-03-14 2020-03-15\n",
"Country/Region \n",
+ "Congo (Brazzaville) 0 1\n",
"Congo (Kinshasa) 2 2\n",
"Cruise Ship 696 696\n",
- "Curacao 0 1\n",
- "Eswatini 0 1\n",
- "French Guiana 5 5\n",
- "Guadeloupe 1 1\n",
+ "Curacao 1 1\n",
+ "Eswatini 1 1\n",
+ "Guadeloupe 1 3\n",
"Holy See 1 1\n",
- "Martinique 3 9\n",
+ "Martinique 9 9\n",
"North Macedonia 14 14\n",
- "Reunion 5 6\n",
+ "Reunion 6 7\n",
"occupied Palestinian territory 0 0"
]
},
@@ -425,10 +425,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.00976,
- "end_time": "2020-03-15T16:43:49.816102",
+ "duration": 0.009916,
+ "end_time": "2020-03-16T19:41:42.118533",
"exception": false,
- "start_time": "2020-03-15T16:43:49.806342",
+ "start_time": "2020-03-16T19:41:42.108617",
"status": "completed"
},
"tags": []
@@ -442,10 +442,10 @@
"execution_count": 11,
"metadata": {
"papermill": {
- "duration": 0.029533,
- "end_time": "2020-03-15T16:43:49.853512",
+ "duration": 0.033068,
+ "end_time": "2020-03-16T19:41:42.159802",
"exception": false,
- "start_time": "2020-03-15T16:43:49.823979",
+ "start_time": "2020-03-16T19:41:42.126734",
"status": "completed"
},
"tags": []
@@ -477,20 +477,20 @@
"version": "3.7.6"
},
"papermill": {
- "duration": 2.036815,
- "end_time": "2020-03-15T16:43:50.175740",
+ "duration": 1.96386,
+ "end_time": "2020-03-16T19:41:42.484999",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/262jiqqx/notebooks/CompileGeoData.ipynb",
+ "input_path": "/tmp/q9ufv19r/notebooks/CompileGeoData.ipynb",
"output_path": "runs/CompileGeoData.run.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/262jiqqx/notebooks/CompileGeoData.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/q9ufv19r/notebooks/CompileGeoData.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/CompileGeoData.run.ipynb",
"out_folder": "data/geodata",
- "ts_folder": "/tmp/262jiqqx/data/covid-19_jhu-csse",
- "worldmap_path": "/tmp/262jiqqx/data/worldmap/country_centroids.csv"
+ "ts_folder": "/tmp/q9ufv19r/data/covid-19_jhu-csse",
+ "worldmap_path": "/tmp/q9ufv19r/data/worldmap/country_centroids.csv"
},
- "start_time": "2020-03-15T16:43:48.138925",
+ "start_time": "2020-03-16T19:41:40.521139",
"version": "1.1.0"
}
},
diff --git a/runs/Dashboard.run.ipynb b/runs/Dashboard.run.ipynb
index 66497b8956654a40180f4d0bf811e8eaa47fcfda..0d70df9325b6d4587f6a863e4e6a1268b1e629dd 100644
--- a/runs/Dashboard.run.ipynb
+++ b/runs/Dashboard.run.ipynb
@@ -5,10 +5,10 @@
"execution_count": 1,
"metadata": {
"papermill": {
- "duration": 0.464711,
- "end_time": "2020-03-16T19:37:31.538772",
+ "duration": 0.51089,
+ "end_time": "2020-03-16T19:41:37.453815",
"exception": false,
- "start_time": "2020-03-16T19:37:31.074061",
+ "start_time": "2020-03-16T19:41:36.942925",
"status": "completed"
},
"tags": []
@@ -27,10 +27,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.02108,
- "end_time": "2020-03-16T19:37:31.579658",
+ "duration": 0.025482,
+ "end_time": "2020-03-16T19:41:37.500197",
"exception": false,
- "start_time": "2020-03-16T19:37:31.558578",
+ "start_time": "2020-03-16T19:41:37.474715",
"status": "completed"
},
"tags": [
@@ -51,10 +51,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.024374,
- "end_time": "2020-03-16T19:37:31.614444",
+ "duration": 0.023622,
+ "end_time": "2020-03-16T19:41:37.537518",
"exception": false,
- "start_time": "2020-03-16T19:37:31.590070",
+ "start_time": "2020-03-16T19:41:37.513896",
"status": "completed"
},
"tags": [
@@ -64,11 +64,11 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/30edqohi/notebooks/Dashboard.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/75ghi30n/notebooks/Dashboard.ipynb\"\n",
"PAPERMILL_OUTPUT_PATH = \"runs/Dashboard.run.ipynb\"\n",
- "ts_folder = \"/tmp/30edqohi/data/covid-19_jhu-csse\"\n",
- "rates_folder = \"/tmp/30edqohi/data/covid-19_rates\"\n",
- "geodata_path = \"/tmp/30edqohi/data/geodata/geo_data.csv\"\n"
+ "ts_folder = \"/tmp/75ghi30n/data/covid-19_jhu-csse\"\n",
+ "rates_folder = \"/tmp/75ghi30n/data/covid-19_rates\"\n",
+ "geodata_path = \"/tmp/75ghi30n/data/geodata/geo_data.csv\"\n"
]
},
{
@@ -76,10 +76,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.024105,
- "end_time": "2020-03-16T19:37:31.660498",
+ "duration": 0.022021,
+ "end_time": "2020-03-16T19:41:37.570812",
"exception": false,
- "start_time": "2020-03-16T19:37:31.636393",
+ "start_time": "2020-03-16T19:41:37.548791",
"status": "completed"
},
"tags": []
@@ -94,10 +94,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.113797,
- "end_time": "2020-03-16T19:37:31.785101",
+ "duration": 0.112261,
+ "end_time": "2020-03-16T19:41:37.693619",
"exception": false,
- "start_time": "2020-03-16T19:37:31.671304",
+ "start_time": "2020-03-16T19:41:37.581358",
"status": "completed"
},
"tags": []
@@ -116,10 +116,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.01115,
- "end_time": "2020-03-16T19:37:31.817527",
+ "duration": 0.009915,
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"exception": false,
- "start_time": "2020-03-16T19:37:31.806377",
+ "start_time": "2020-03-16T19:41:37.710809",
"status": "completed"
},
"tags": []
@@ -137,10 +137,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.038028,
- "end_time": "2020-03-16T19:37:31.864069",
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+ "end_time": "2020-03-16T19:41:37.769598",
"exception": false,
- "start_time": "2020-03-16T19:37:31.826041",
+ "start_time": "2020-03-16T19:41:37.729249",
"status": "completed"
},
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@@ -149,7 +149,7 @@
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+ " const outputDiv = document.getElementById(\"altair-viz-f01f68a2797d44d3bcb2682fe9892cb7\");\n",
" const paths = {\n",
" \"vega\": \"https://cdn.jsdelivr.net/npm//vega@5?noext\",\n",
" \"vega-lib\": \"https://cdn.jsdelivr.net/npm//vega-lib?noext\",\n",
@@ -732,7 +732,7 @@
" .catch(showError)\n",
" .then(() => displayChart(vegaEmbed));\n",
" }\n",
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"</script>"
],
"text/plain": [
@@ -910,20 +910,20 @@
"version": "3.7.6"
},
"papermill": {
- "duration": 3.523833,
- "end_time": "2020-03-16T19:37:33.679489",
+ "duration": 3.510491,
+ "end_time": "2020-03-16T19:41:39.592874",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/30edqohi/notebooks/Dashboard.ipynb",
+ "input_path": "/tmp/75ghi30n/notebooks/Dashboard.ipynb",
"output_path": "runs/Dashboard.run.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/30edqohi/notebooks/Dashboard.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/75ghi30n/notebooks/Dashboard.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/Dashboard.run.ipynb",
- "geodata_path": "/tmp/30edqohi/data/geodata/geo_data.csv",
- "rates_folder": "/tmp/30edqohi/data/covid-19_rates",
- "ts_folder": "/tmp/30edqohi/data/covid-19_jhu-csse"
+ "geodata_path": "/tmp/75ghi30n/data/geodata/geo_data.csv",
+ "rates_folder": "/tmp/75ghi30n/data/covid-19_rates",
+ "ts_folder": "/tmp/75ghi30n/data/covid-19_jhu-csse"
},
- "start_time": "2020-03-16T19:37:30.155656",
+ "start_time": "2020-03-16T19:41:36.082383",
"version": "1.1.0"
}
},