From d20d834d65f526d697e5eae9e22bdfd59aa54ac3 Mon Sep 17 00:00:00 2001
From: Chandrasekhar Ramakrishnan <cramakri@ethz.ch>
Date: Wed, 18 Mar 2020 17:41:18 +0000
Subject: [PATCH] renku run papermill -p ts_folder ./data/covid-19_jhu-csse/ -p
wb_path ./data/worldbank/SP.POP.TOTL.zip -p geodata_path
./data/geodata/geo_data.csv -p out_folder ./data/covid-19_rates/
--inject-paths notebooks/process/ToRates.ipynb runs/ToRates.run.ipynb
---
...ffbbb1264ae2a646824c0fd83a20_papermill.cwl | 137 ++++++++
.../ts_rates_19-covid-confirmed.csv | 4 +-
.../ts_rates_19-covid-deaths.csv | 4 +-
.../ts_rates_19-covid-recovered.csv | 4 +-
runs/ToRates.run.ipynb | 309 ++++++++++--------
5 files changed, 307 insertions(+), 151 deletions(-)
create mode 100644 .renku/workflow/7f7dffbbb1264ae2a646824c0fd83a20_papermill.cwl
diff --git a/.renku/workflow/7f7dffbbb1264ae2a646824c0fd83a20_papermill.cwl b/.renku/workflow/7f7dffbbb1264ae2a646824c0fd83a20_papermill.cwl
new file mode 100644
index 00000000..988afcd8
--- /dev/null
+++ b/.renku/workflow/7f7dffbbb1264ae2a646824c0fd83a20_papermill.cwl
@@ -0,0 +1,137 @@
+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_10:
+ default: runs/ToRates.run.ipynb
+ inputBinding:
+ position: 10
+ 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: wb_path
+ inputBinding:
+ position: 3
+ prefix: -p
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_4:
+ default:
+ class: File
+ path: ../../data/worldbank/SP.POP.TOTL.zip
+ inputBinding:
+ position: 4
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: File
+ input_5:
+ default: geodata_path
+ inputBinding:
+ position: 5
+ prefix: -p
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_6:
+ default:
+ class: File
+ path: ../../data/geodata/geo_data.csv
+ inputBinding:
+ position: 6
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: File
+ input_7:
+ default: out_folder
+ inputBinding:
+ position: 7
+ prefix: -p
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_8:
+ default: data/covid-19_rates
+ inputBinding:
+ position: 8
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_9:
+ default:
+ class: File
+ path: ../../notebooks/process/ToRates.ipynb
+ inputBinding:
+ position: 9
+ prefix: --inject-paths
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: File
+outputs:
+ output_0:
+ outputBinding:
+ glob: $(inputs.input_10)
+ streamable: false
+ type: File
+ output_1:
+ outputBinding:
+ glob: $(inputs.input_8)
+ streamable: false
+ type: Directory
+permanentFailCodes: []
+requirements:
+- class: InlineJavascriptRequirement
+- class: InitialWorkDirRequirement
+ listing:
+ - entry: '$({"listing": [], "class": "Directory"})'
+ entryname: runs
+ writable: true
+ - entry: '$({"listing": [], "class": "Directory"})'
+ entryname: data/covid-19_rates
+ writable: true
+ - entry: $(inputs.input_2)
+ entryname: data/covid-19_jhu-csse
+ writable: false
+ - entry: $(inputs.input_4)
+ entryname: data/worldbank/SP.POP.TOTL.zip
+ writable: false
+ - entry: $(inputs.input_6)
+ entryname: data/geodata/geo_data.csv
+ writable: false
+ - entry: $(inputs.input_9)
+ entryname: notebooks/process/ToRates.ipynb
+ writable: false
+successCodes: []
+temporaryFailCodes: []
diff --git a/data/covid-19_rates/ts_rates_19-covid-confirmed.csv b/data/covid-19_rates/ts_rates_19-covid-confirmed.csv
index 56d95691..525bf8a3 100644
--- a/data/covid-19_rates/ts_rates_19-covid-confirmed.csv
+++ b/data/covid-19_rates/ts_rates_19-covid-confirmed.csv
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:eaf597680f5c0173a9df77b542cbd0b135b864014570eb8e246f2e227bf17109
-size 69756
+oid sha256:d32a8416d35d973167ab29853bd039e1b056c1d616b3388fa13c36d561505cfb
+size 80315
diff --git a/data/covid-19_rates/ts_rates_19-covid-deaths.csv b/data/covid-19_rates/ts_rates_19-covid-deaths.csv
index 1be0fd31..9b7466e7 100644
--- a/data/covid-19_rates/ts_rates_19-covid-deaths.csv
+++ b/data/covid-19_rates/ts_rates_19-covid-deaths.csv
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:1add0765faacbf0777043b63e5f52884dbcc58b0e744fc602fe9d07009905fca
-size 39014
+oid sha256:366c29eb309d7a5545d01f4cebc458d3c5e7150e0a3699779c35b383e100e236
+size 45495
diff --git a/data/covid-19_rates/ts_rates_19-covid-recovered.csv b/data/covid-19_rates/ts_rates_19-covid-recovered.csv
index eb1ebf6c..11cd8c91 100644
--- a/data/covid-19_rates/ts_rates_19-covid-recovered.csv
+++ b/data/covid-19_rates/ts_rates_19-covid-recovered.csv
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:261c4036d5485dc919439f403b3f743142e9953117796e53afd2ee1175f3579e
-size 49919
+oid sha256:b906aa714823501ad73cb07b108b63062181c547b30b3744eeaf85aca2032845
+size 57465
diff --git a/runs/ToRates.run.ipynb b/runs/ToRates.run.ipynb
index 0a30ca67..1f940285 100644
--- a/runs/ToRates.run.ipynb
+++ b/runs/ToRates.run.ipynb
@@ -4,10 +4,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.024961,
- "end_time": "2020-03-15T18:37:31.040525",
+ "duration": 0.019248,
+ "end_time": "2020-03-18T17:41:16.247818",
"exception": false,
- "start_time": "2020-03-15T18:37:31.015564",
+ "start_time": "2020-03-18T17:41:16.228570",
"status": "completed"
},
"tags": []
@@ -21,10 +21,10 @@
"execution_count": 1,
"metadata": {
"papermill": {
- "duration": 0.301514,
- "end_time": "2020-03-15T18:37:31.355857",
+ "duration": 0.345001,
+ "end_time": "2020-03-18T17:41:16.607949",
"exception": false,
- "start_time": "2020-03-15T18:37:31.054343",
+ "start_time": "2020-03-18T17:41:16.262948",
"status": "completed"
},
"tags": []
@@ -40,10 +40,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.024072,
- "end_time": "2020-03-15T18:37:31.401335",
+ "duration": 0.025568,
+ "end_time": "2020-03-18T17:41:16.652301",
"exception": false,
- "start_time": "2020-03-15T18:37:31.377263",
+ "start_time": "2020-03-18T17:41:16.626733",
"status": "completed"
},
"tags": [
@@ -64,10 +64,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.024999,
- "end_time": "2020-03-15T18:37:31.439386",
+ "duration": 0.02526,
+ "end_time": "2020-03-18T17:41:16.692448",
"exception": false,
- "start_time": "2020-03-15T18:37:31.414387",
+ "start_time": "2020-03-18T17:41:16.667188",
"status": "completed"
},
"tags": [
@@ -77,22 +77,22 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/fsb4wn_r/notebooks/ToRates.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"notebooks/process/ToRates.ipynb\"\n",
"PAPERMILL_OUTPUT_PATH = \"runs/ToRates.run.ipynb\"\n",
- "ts_folder = \"/tmp/fsb4wn_r/data/covid-19_jhu-csse\"\n",
- "wb_path = \"/tmp/fsb4wn_r/data/worldbank/SP.POP.TOTL.zip\"\n",
- "geodata_path = \"/tmp/fsb4wn_r/data/geodata/geo_data.csv\"\n",
- "out_folder = \"data/covid-19_rates\"\n"
+ "ts_folder = \"./data/covid-19_jhu-csse/\"\n",
+ "wb_path = \"./data/worldbank/SP.POP.TOTL.zip\"\n",
+ "geodata_path = \"./data/geodata/geo_data.csv\"\n",
+ "out_folder = \"./data/covid-19_rates/\"\n"
]
},
{
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.010544,
- "end_time": "2020-03-15T18:37:31.463234",
+ "duration": 0.013342,
+ "end_time": "2020-03-18T17:41:16.721760",
"exception": false,
- "start_time": "2020-03-15T18:37:31.452690",
+ "start_time": "2020-03-18T17:41:16.708418",
"status": "completed"
},
"tags": [
@@ -110,10 +110,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.030699,
- "end_time": "2020-03-15T18:37:31.504252",
+ "duration": 0.030827,
+ "end_time": "2020-03-18T17:41:16.766227",
"exception": false,
- "start_time": "2020-03-15T18:37:31.473553",
+ "start_time": "2020-03-18T17:41:16.735400",
"status": "completed"
},
"tags": []
@@ -135,10 +135,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.130448,
- "end_time": "2020-03-15T18:37:31.650988",
+ "duration": 0.169334,
+ "end_time": "2020-03-18T17:41:16.952367",
"exception": false,
- "start_time": "2020-03-15T18:37:31.520540",
+ "start_time": "2020-03-18T17:41:16.783033",
"status": "completed"
},
"tags": []
@@ -156,10 +156,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.022829,
- "end_time": "2020-03-15T18:37:31.697981",
+ "duration": 0.013234,
+ "end_time": "2020-03-18T17:41:16.984067",
"exception": false,
- "start_time": "2020-03-15T18:37:31.675152",
+ "start_time": "2020-03-18T17:41:16.970833",
"status": "completed"
},
"tags": []
@@ -173,10 +173,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.047034,
- "end_time": "2020-03-15T18:37:31.756497",
+ "duration": 0.042152,
+ "end_time": "2020-03-18T17:41:17.039652",
"exception": false,
- "start_time": "2020-03-15T18:37:31.709463",
+ "start_time": "2020-03-18T17:41:16.997500",
"status": "completed"
},
"tags": []
@@ -192,10 +192,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.011097,
- "end_time": "2020-03-15T18:37:31.790107",
+ "duration": 0.013053,
+ "end_time": "2020-03-18T17:41:17.069282",
"exception": false,
- "start_time": "2020-03-15T18:37:31.779010",
+ "start_time": "2020-03-18T17:41:17.056229",
"status": "completed"
},
"tags": []
@@ -209,10 +209,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.063536,
- "end_time": "2020-03-15T18:37:31.862736",
+ "duration": 0.067991,
+ "end_time": "2020-03-18T17:41:17.150655",
"exception": false,
- "start_time": "2020-03-15T18:37:31.799200",
+ "start_time": "2020-03-18T17:41:17.082664",
"status": "completed"
},
"tags": []
@@ -345,10 +345,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.010344,
- "end_time": "2020-03-15T18:37:31.891117",
+ "duration": 0.013804,
+ "end_time": "2020-03-18T17:41:17.183019",
"exception": false,
- "start_time": "2020-03-15T18:37:31.880773",
+ "start_time": "2020-03-18T17:41:17.169215",
"status": "completed"
},
"tags": []
@@ -362,10 +362,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.027744,
- "end_time": "2020-03-15T18:37:31.928366",
+ "duration": 0.035748,
+ "end_time": "2020-03-18T17:41:17.232910",
"exception": false,
- "start_time": "2020-03-15T18:37:31.900622",
+ "start_time": "2020-03-18T17:41:17.197162",
"status": "completed"
},
"tags": []
@@ -394,10 +394,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.020322,
- "end_time": "2020-03-15T18:37:31.963446",
+ "duration": 0.025899,
+ "end_time": "2020-03-18T17:41:17.276983",
"exception": false,
- "start_time": "2020-03-15T18:37:31.943124",
+ "start_time": "2020-03-18T17:41:17.251084",
"status": "completed"
},
"tags": []
@@ -412,10 +412,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.010478,
- "end_time": "2020-03-15T18:37:31.984626",
+ "duration": 0.014096,
+ "end_time": "2020-03-18T17:41:17.304846",
"exception": false,
- "start_time": "2020-03-15T18:37:31.974148",
+ "start_time": "2020-03-18T17:41:17.290750",
"status": "completed"
},
"tags": []
@@ -429,10 +429,10 @@
"execution_count": 10,
"metadata": {
"papermill": {
- "duration": 0.047267,
- "end_time": "2020-03-15T18:37:32.042700",
+ "duration": 0.042745,
+ "end_time": "2020-03-18T17:41:17.362191",
"exception": false,
- "start_time": "2020-03-15T18:37:31.995433",
+ "start_time": "2020-03-18T17:41:17.319446",
"status": "completed"
},
"tags": []
@@ -461,8 +461,8 @@
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
- " <th>2020-03-13 00:00:00</th>\n",
- " <th>2020-03-14 00:00:00</th>\n",
+ " <th>2020-03-16 00:00:00</th>\n",
+ " <th>2020-03-17 00:00:00</th>\n",
" </tr>\n",
" <tr>\n",
" <th>Country/Region</th>\n",
@@ -474,11 +474,18 @@
" </thead>\n",
" <tbody>\n",
" <tr>\n",
+ " <th>Congo (Brazzaville)</th>\n",
+ " <th>21.7587</th>\n",
+ " <th>-4.0383</th>\n",
+ " <td>1</td>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
" <th>Congo (Kinshasa)</th>\n",
" <th>21.7587</th>\n",
" <th>-4.0383</th>\n",
" <td>2</td>\n",
- " <td>2</td>\n",
+ " <td>3</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Cruise Ship</th>\n",
@@ -488,24 +495,10 @@
" <td>696</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>French Guiana</th>\n",
- " <th>-53.1258</th>\n",
- " <th>3.9339</th>\n",
- " <td>5</td>\n",
- " <td>5</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>Guadeloupe</th>\n",
- " <th>-61.5510</th>\n",
- " <th>16.2650</th>\n",
- " <td>1</td>\n",
- " <td>1</td>\n",
- " </tr>\n",
- " <tr>\n",
" <th>Guernsey</th>\n",
" <th>-2.5800</th>\n",
" <th>49.4500</th>\n",
- " <td>0</td>\n",
+ " <td>1</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
@@ -519,96 +512,103 @@
" <th>Jersey</th>\n",
" <th>-2.1100</th>\n",
" <th>49.1900</th>\n",
- " <td>0</td>\n",
+ " <td>2</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Martinique</th>\n",
" <th>-61.0242</th>\n",
" <th>14.6415</th>\n",
- " <td>3</td>\n",
- " <td>9</td>\n",
+ " <td>15</td>\n",
+ " <td>16</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>Reunion</th>\n",
- " <th>55.5364</th>\n",
- " <th>-21.1151</th>\n",
- " <td>5</td>\n",
- " <td>6</td>\n",
+ " <th>Republic of the Congo</th>\n",
+ " <th>15.5560</th>\n",
+ " <th>-1.4400</th>\n",
+ " <td>1</td>\n",
+ " <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Saint Lucia</th>\n",
" <th>-60.9789</th>\n",
" <th>13.9094</th>\n",
- " <td>0</td>\n",
- " <td>1</td>\n",
+ " <td>2</td>\n",
+ " <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Saint Vincent and the Grenadines</th>\n",
" <th>-61.2872</th>\n",
" <th>12.9843</th>\n",
- " <td>0</td>\n",
+ " <td>1</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Taiwan*</th>\n",
" <th>121.0000</th>\n",
" <th>23.7000</th>\n",
- " <td>50</td>\n",
- " <td>53</td>\n",
+ " <td>67</td>\n",
+ " <td>77</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>Venezuela</th>\n",
- " <th>-66.5897</th>\n",
- " <th>6.4238</th>\n",
- " <td>0</td>\n",
- " <td>2</td>\n",
+ " <th>The Bahamas</th>\n",
+ " <th>-76.0000</th>\n",
+ " <th>24.2500</th>\n",
+ " <td>1</td>\n",
+ " <td>1</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>occupied Palestinian territory</th>\n",
- " <th>35.2332</th>\n",
- " <th>31.9522</th>\n",
- " <td>0</td>\n",
+ " <th>The Gambia</th>\n",
+ " <th>-16.6000</th>\n",
+ " <th>13.4667</th>\n",
" <td>0</td>\n",
+ " <td>1</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Venezuela</th>\n",
+ " <th>-66.5897</th>\n",
+ " <th>6.4238</th>\n",
+ " <td>17</td>\n",
+ " <td>33</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
- " 2020-03-13 00:00:00 \\\n",
+ " 2020-03-16 00:00:00 \\\n",
"Country/Region Long Lat \n",
+ "Congo (Brazzaville) 21.7587 -4.0383 1 \n",
"Congo (Kinshasa) 21.7587 -4.0383 2 \n",
"Cruise Ship 139.6380 35.4437 696 \n",
- "French Guiana -53.1258 3.9339 5 \n",
- "Guadeloupe -61.5510 16.2650 1 \n",
- "Guernsey -2.5800 49.4500 0 \n",
+ "Guernsey -2.5800 49.4500 1 \n",
"Holy See 12.4534 41.9029 1 \n",
- "Jersey -2.1100 49.1900 0 \n",
- "Martinique -61.0242 14.6415 3 \n",
- "Reunion 55.5364 -21.1151 5 \n",
- "Saint Lucia -60.9789 13.9094 0 \n",
- "Saint Vincent and the Grenadines -61.2872 12.9843 0 \n",
- "Taiwan* 121.0000 23.7000 50 \n",
- "Venezuela -66.5897 6.4238 0 \n",
- "occupied Palestinian territory 35.2332 31.9522 0 \n",
+ "Jersey -2.1100 49.1900 2 \n",
+ "Martinique -61.0242 14.6415 15 \n",
+ "Republic of the Congo 15.5560 -1.4400 1 \n",
+ "Saint Lucia -60.9789 13.9094 2 \n",
+ "Saint Vincent and the Grenadines -61.2872 12.9843 1 \n",
+ "Taiwan* 121.0000 23.7000 67 \n",
+ "The Bahamas -76.0000 24.2500 1 \n",
+ "The Gambia -16.6000 13.4667 0 \n",
+ "Venezuela -66.5897 6.4238 17 \n",
"\n",
- " 2020-03-14 00:00:00 \n",
+ " 2020-03-17 00:00:00 \n",
"Country/Region Long Lat \n",
- "Congo (Kinshasa) 21.7587 -4.0383 2 \n",
+ "Congo (Brazzaville) 21.7587 -4.0383 1 \n",
+ "Congo (Kinshasa) 21.7587 -4.0383 3 \n",
"Cruise Ship 139.6380 35.4437 696 \n",
- "French Guiana -53.1258 3.9339 5 \n",
- "Guadeloupe -61.5510 16.2650 1 \n",
"Guernsey -2.5800 49.4500 1 \n",
"Holy See 12.4534 41.9029 1 \n",
"Jersey -2.1100 49.1900 2 \n",
- "Martinique -61.0242 14.6415 9 \n",
- "Reunion 55.5364 -21.1151 6 \n",
- "Saint Lucia -60.9789 13.9094 1 \n",
+ "Martinique -61.0242 14.6415 16 \n",
+ "Republic of the Congo 15.5560 -1.4400 1 \n",
+ "Saint Lucia -60.9789 13.9094 2 \n",
"Saint Vincent and the Grenadines -61.2872 12.9843 1 \n",
- "Taiwan* 121.0000 23.7000 53 \n",
- "Venezuela -66.5897 6.4238 2 \n",
- "occupied Palestinian territory 35.2332 31.9522 0 "
+ "Taiwan* 121.0000 23.7000 77 \n",
+ "The Bahamas -76.0000 24.2500 1 \n",
+ "The Gambia -16.6000 13.4667 1 \n",
+ "Venezuela -66.5897 6.4238 33 "
]
},
"execution_count": 10,
@@ -626,10 +626,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.011403,
- "end_time": "2020-03-15T18:37:32.074357",
+ "duration": 0.014536,
+ "end_time": "2020-03-18T17:41:17.393746",
"exception": false,
- "start_time": "2020-03-15T18:37:32.062954",
+ "start_time": "2020-03-18T17:41:17.379210",
"status": "completed"
},
"tags": []
@@ -643,10 +643,10 @@
"execution_count": 11,
"metadata": {
"papermill": {
- "duration": 0.036638,
- "end_time": "2020-03-15T18:37:32.121372",
+ "duration": 0.039612,
+ "end_time": "2020-03-18T17:41:17.450122",
"exception": false,
- "start_time": "2020-03-15T18:37:32.084734",
+ "start_time": "2020-03-18T17:41:17.410510",
"status": "completed"
},
"tags": []
@@ -660,10 +660,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.010241,
- "end_time": "2020-03-15T18:37:32.149495",
+ "duration": 0.01421,
+ "end_time": "2020-03-18T17:41:17.480878",
"exception": false,
- "start_time": "2020-03-15T18:37:32.139254",
+ "start_time": "2020-03-18T17:41:17.466668",
"status": "completed"
},
"tags": []
@@ -677,10 +677,10 @@
"execution_count": 12,
"metadata": {
"papermill": {
- "duration": 0.049287,
- "end_time": "2020-03-15T18:37:32.209471",
+ "duration": 0.084227,
+ "end_time": "2020-03-18T17:41:17.579746",
"exception": false,
- "start_time": "2020-03-15T18:37:32.160184",
+ "start_time": "2020-03-18T17:41:17.495519",
"status": "completed"
},
"tags": []
@@ -747,6 +747,19 @@
" <td>49.468098</td>\n",
" </tr>\n",
" <tr>\n",
+ " <th>The Gambia</th>\n",
+ " <td>Gambia</td>\n",
+ " <td>The Gambia</td>\n",
+ " <td>Africa</td>\n",
+ " <td>Western Africa</td>\n",
+ " <td>Sub-Saharan Africa</td>\n",
+ " <td>1782893</td>\n",
+ " <td>2272.0</td>\n",
+ " <td>5. Low income</td>\n",
+ " <td>-15.396013</td>\n",
+ " <td>13.449652</td>\n",
+ " </tr>\n",
+ " <tr>\n",
" <th>Jersey</th>\n",
" <td>Jersey</td>\n",
" <td>Jersey</td>\n",
@@ -819,6 +832,7 @@
" name \\\n",
"name_jhu \n",
"Guernsey Guernsey \n",
+ "The Gambia Gambia \n",
"Jersey Jersey \n",
"Saint Lucia Saint Lucia \n",
"Taiwan* Taiwan \n",
@@ -828,6 +842,7 @@
" name_long region_un \\\n",
"name_jhu \n",
"Guernsey Guernsey Europe \n",
+ "The Gambia The Gambia Africa \n",
"Jersey Jersey Europe \n",
"Saint Lucia Saint Lucia Americas \n",
"Taiwan* Taiwan Asia \n",
@@ -837,6 +852,7 @@
" subregion region_wb \\\n",
"name_jhu \n",
"Guernsey Northern Europe Europe & Central Asia \n",
+ "The Gambia Western Africa Sub-Saharan Africa \n",
"Jersey Northern Europe Europe & Central Asia \n",
"Saint Lucia Caribbean Latin America & Caribbean \n",
"Taiwan* Eastern Asia East Asia & Pacific \n",
@@ -846,6 +862,7 @@
" pop_est gdp_md_est \\\n",
"name_jhu \n",
"Guernsey 68633 2742.0 \n",
+ "The Gambia 1782893 2272.0 \n",
"Jersey 91626 5100.0 \n",
"Saint Lucia 160267 1778.0 \n",
"Taiwan* 22974347 712000.0 \n",
@@ -855,6 +872,7 @@
" income_grp Longitude \\\n",
"name_jhu \n",
"Guernsey 2. High income: nonOECD -2.572391 \n",
+ "The Gambia 5. Low income -15.396013 \n",
"Jersey 2. High income: nonOECD -2.126899 \n",
"Saint Lucia 3. Upper middle income -60.969699 \n",
"Taiwan* 2. High income: nonOECD 120.954273 \n",
@@ -864,6 +882,7 @@
" Latitude \n",
"name_jhu \n",
"Guernsey 49.468098 \n",
+ "The Gambia 13.449652 \n",
"Jersey 49.218374 \n",
"Saint Lucia 13.894795 \n",
"Taiwan* 23.753993 \n",
@@ -889,10 +908,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.011342,
- "end_time": "2020-03-15T18:37:32.242689",
+ "duration": 0.015412,
+ "end_time": "2020-03-18T17:41:17.614936",
"exception": false,
- "start_time": "2020-03-15T18:37:32.231347",
+ "start_time": "2020-03-18T17:41:17.599524",
"status": "completed"
},
"tags": []
@@ -906,10 +925,10 @@
"execution_count": 13,
"metadata": {
"papermill": {
- "duration": 0.079225,
- "end_time": "2020-03-15T18:37:32.333345",
+ "duration": 0.046955,
+ "end_time": "2020-03-18T17:41:17.678221",
"exception": false,
- "start_time": "2020-03-15T18:37:32.254120",
+ "start_time": "2020-03-18T17:41:17.631266",
"status": "completed"
},
"tags": []
@@ -934,10 +953,10 @@
"execution_count": 14,
"metadata": {
"papermill": {
- "duration": 0.05118,
- "end_time": "2020-03-15T18:37:32.407865",
+ "duration": 0.074084,
+ "end_time": "2020-03-18T17:41:17.772067",
"exception": false,
- "start_time": "2020-03-15T18:37:32.356685",
+ "start_time": "2020-03-18T17:41:17.697983",
"status": "completed"
},
"tags": []
@@ -970,21 +989,21 @@
"version": "3.7.6"
},
"papermill": {
- "duration": 2.574464,
- "end_time": "2020-03-15T18:37:32.738690",
+ "duration": 2.764452,
+ "end_time": "2020-03-18T17:41:18.108751",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/fsb4wn_r/notebooks/ToRates.ipynb",
+ "input_path": "notebooks/process/ToRates.ipynb",
"output_path": "runs/ToRates.run.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/fsb4wn_r/notebooks/ToRates.ipynb",
+ "PAPERMILL_INPUT_PATH": "notebooks/process/ToRates.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/ToRates.run.ipynb",
- "geodata_path": "/tmp/fsb4wn_r/data/geodata/geo_data.csv",
- "out_folder": "data/covid-19_rates",
- "ts_folder": "/tmp/fsb4wn_r/data/covid-19_jhu-csse",
- "wb_path": "/tmp/fsb4wn_r/data/worldbank/SP.POP.TOTL.zip"
+ "geodata_path": "./data/geodata/geo_data.csv",
+ "out_folder": "./data/covid-19_rates/",
+ "ts_folder": "./data/covid-19_jhu-csse/",
+ "wb_path": "./data/worldbank/SP.POP.TOTL.zip"
},
- "start_time": "2020-03-15T18:37:30.164226",
+ "start_time": "2020-03-18T17:41:15.344299",
"version": "1.1.0"
}
},
--
GitLab