diff --git a/.renku/workflow/342d5ac23ef74852a0ecfa61ff854182_papermill.cwl b/.renku/workflow/342d5ac23ef74852a0ecfa61ff854182_papermill.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..988afcd830a1f9c81a2ca1b826ac4fbb0f595b33
--- /dev/null
+++ b/.renku/workflow/342d5ac23ef74852a0ecfa61ff854182_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 98887063f5365f15ed1f3390c83b88431cf54374..15575de4fcec2e42e9f2433cffd90ccdfd55fd16 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:cd7f729f54a2d71b1f2cd34c0b6518cf8df786c8fea55c7f2de9f1f072ab154c
-size 113607
+oid sha256:cda52059dddf7d5b27213022f624ba1cbcb804e5ad54c7046817274dbe160a6b
+size 123180
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 92936d14841fb86550fffb5b7408ed322015601c..d5d76eef4a99e85577b04d3fcee588d924f8220f 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:e862e93839d050845736c86f11de1f6568ede7bbb5475e9540c20d88e2dda8ab
-size 68873
+oid sha256:97987cd3c3e0093de8ca84d4c9bc38343dca820135834b6ee1965bddfbe06ddd
+size 76222
diff --git a/runs/ToRates.run.ipynb b/runs/ToRates.run.ipynb
index 979f74c0c1356dbb10f64343a6cb1911049de69c..0bad18201ebd7033d233a66825a41957ae3044cd 100644
--- a/runs/ToRates.run.ipynb
+++ b/runs/ToRates.run.ipynb
@@ -4,10 +4,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.020969,
- "end_time": "2020-03-27T08:23:23.700948",
+ "duration": 0.027314,
+ "end_time": "2020-03-30T09:42:38.217502",
"exception": false,
- "start_time": "2020-03-27T08:23:23.679979",
+ "start_time": "2020-03-30T09:42:38.190188",
"status": "completed"
},
"tags": []
@@ -21,10 +21,10 @@
"execution_count": 1,
"metadata": {
"papermill": {
- "duration": 0.332743,
- "end_time": "2020-03-27T08:23:24.048007",
+ "duration": 0.366708,
+ "end_time": "2020-03-30T09:42:38.596336",
"exception": false,
- "start_time": "2020-03-27T08:23:23.715264",
+ "start_time": "2020-03-30T09:42:38.229628",
"status": "completed"
},
"tags": []
@@ -40,10 +40,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.024048,
- "end_time": "2020-03-27T08:23:24.087404",
+ "duration": 0.027731,
+ "end_time": "2020-03-30T09:42:38.646131",
"exception": false,
- "start_time": "2020-03-27T08:23:24.063356",
+ "start_time": "2020-03-30T09:42:38.618400",
"status": "completed"
},
"tags": [
@@ -64,10 +64,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.026683,
- "end_time": "2020-03-27T08:23:24.130000",
+ "duration": 0.025036,
+ "end_time": "2020-03-30T09:42:38.685373",
"exception": false,
- "start_time": "2020-03-27T08:23:24.103317",
+ "start_time": "2020-03-30T09:42:38.660337",
"status": "completed"
},
"tags": [
@@ -77,22 +77,22 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/qa77nd3o/notebooks/process/ToRates.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"notebooks/process/ToRates.ipynb\"\n",
"PAPERMILL_OUTPUT_PATH = \"runs/ToRates.run.ipynb\"\n",
- "ts_folder = \"/tmp/qa77nd3o/data/covid-19_jhu-csse\"\n",
- "wb_path = \"/tmp/qa77nd3o/data/worldbank/SP.POP.TOTL.zip\"\n",
- "geodata_path = \"/tmp/qa77nd3o/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": 0.012387,
- "end_time": "2020-03-27T08:23:24.158849",
+ "duration": 0.009947,
+ "end_time": "2020-03-30T09:42:38.708257",
"exception": false,
- "start_time": "2020-03-27T08:23:24.146462",
+ "start_time": "2020-03-30T09:42:38.698310",
"status": "completed"
},
"tags": [
@@ -110,10 +110,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.029332,
- "end_time": "2020-03-27T08:23:24.201268",
+ "duration": 0.033081,
+ "end_time": "2020-03-30T09:42:38.752747",
"exception": false,
- "start_time": "2020-03-27T08:23:24.171936",
+ "start_time": "2020-03-30T09:42:38.719666",
"status": "completed"
},
"tags": []
@@ -135,10 +135,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.136002,
- "end_time": "2020-03-27T08:23:24.352626",
+ "duration": 0.113389,
+ "end_time": "2020-03-30T09:42:38.881452",
"exception": false,
- "start_time": "2020-03-27T08:23:24.216624",
+ "start_time": "2020-03-30T09:42:38.768063",
"status": "completed"
},
"tags": []
@@ -155,10 +155,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.012717,
- "end_time": "2020-03-27T08:23:24.381551",
+ "duration": 0.011789,
+ "end_time": "2020-03-30T09:42:38.916551",
"exception": false,
- "start_time": "2020-03-27T08:23:24.368834",
+ "start_time": "2020-03-30T09:42:38.904762",
"status": "completed"
},
"tags": []
@@ -172,10 +172,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.046125,
- "end_time": "2020-03-27T08:23:24.440601",
+ "duration": 0.055136,
+ "end_time": "2020-03-30T09:42:38.981858",
"exception": false,
- "start_time": "2020-03-27T08:23:24.394476",
+ "start_time": "2020-03-30T09:42:38.926722",
"status": "completed"
},
"tags": []
@@ -191,10 +191,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.013966,
- "end_time": "2020-03-27T08:23:24.472536",
+ "duration": 0.011511,
+ "end_time": "2020-03-30T09:42:39.015831",
"exception": false,
- "start_time": "2020-03-27T08:23:24.458570",
+ "start_time": "2020-03-30T09:42:39.004320",
"status": "completed"
},
"tags": []
@@ -208,10 +208,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.068228,
- "end_time": "2020-03-27T08:23:24.553802",
+ "duration": 0.070611,
+ "end_time": "2020-03-30T09:42:39.096641",
"exception": false,
- "start_time": "2020-03-27T08:23:24.485574",
+ "start_time": "2020-03-30T09:42:39.026030",
"status": "completed"
},
"tags": []
@@ -344,10 +344,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.013037,
- "end_time": "2020-03-27T08:23:24.583291",
+ "duration": 0.011332,
+ "end_time": "2020-03-30T09:42:39.129974",
"exception": false,
- "start_time": "2020-03-27T08:23:24.570254",
+ "start_time": "2020-03-30T09:42:39.118642",
"status": "completed"
},
"tags": []
@@ -361,10 +361,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.036114,
- "end_time": "2020-03-27T08:23:24.633027",
+ "duration": 0.042366,
+ "end_time": "2020-03-30T09:42:39.182695",
"exception": false,
- "start_time": "2020-03-27T08:23:24.596913",
+ "start_time": "2020-03-30T09:42:39.140329",
"status": "completed"
},
"tags": []
@@ -393,10 +393,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.025,
- "end_time": "2020-03-27T08:23:24.675848",
+ "duration": 0.025036,
+ "end_time": "2020-03-30T09:42:39.223885",
"exception": false,
- "start_time": "2020-03-27T08:23:24.650848",
+ "start_time": "2020-03-30T09:42:39.198849",
"status": "completed"
},
"tags": []
@@ -411,10 +411,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.017796,
- "end_time": "2020-03-27T08:23:24.708980",
+ "duration": 0.01029,
+ "end_time": "2020-03-30T09:42:39.247229",
"exception": false,
- "start_time": "2020-03-27T08:23:24.691184",
+ "start_time": "2020-03-30T09:42:39.236939",
"status": "completed"
},
"tags": []
@@ -428,10 +428,10 @@
"execution_count": 10,
"metadata": {
"papermill": {
- "duration": 0.045177,
- "end_time": "2020-03-27T08:23:24.771346",
+ "duration": 0.059548,
+ "end_time": "2020-03-30T09:42:39.317750",
"exception": false,
- "start_time": "2020-03-27T08:23:24.726169",
+ "start_time": "2020-03-30T09:42:39.258202",
"status": "completed"
},
"tags": []
@@ -460,8 +460,8 @@
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
- " <th>2020-03-25 00:00:00</th>\n",
- " <th>2020-03-26 00:00:00</th>\n",
+ " <th>2020-03-28 00:00:00</th>\n",
+ " <th>2020-03-29 00:00:00</th>\n",
" </tr>\n",
" <tr>\n",
" <th>Country/Region</th>\n",
@@ -476,22 +476,29 @@
" <th>Bahamas</th>\n",
" <th>-77.396300</th>\n",
" <th>25.034300</th>\n",
- " <td>5</td>\n",
- " <td>9</td>\n",
+ " <td>10</td>\n",
+ " <td>11</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>Burma</th>\n",
+ " <th>95.956000</th>\n",
+ " <th>21.916200</th>\n",
+ " <td>8</td>\n",
+ " <td>10</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Congo (Brazzaville)</th>\n",
" <th>21.758700</th>\n",
" <th>-4.038300</th>\n",
" <td>4</td>\n",
- " <td>4</td>\n",
+ " <td>19</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Congo (Kinshasa)</th>\n",
" <th>21.758700</th>\n",
" <th>-4.038300</th>\n",
- " <td>48</td>\n",
- " <td>51</td>\n",
+ " <td>65</td>\n",
+ " <td>65</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Diamond Princess</th>\n",
@@ -505,28 +512,35 @@
" <th>-15.310100</th>\n",
" <th>13.443200</th>\n",
" <td>3</td>\n",
- " <td>3</td>\n",
+ " <td>4</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Holy See</th>\n",
" <th>12.453400</th>\n",
" <th>41.902900</th>\n",
- " <td>4</td>\n",
- " <td>4</td>\n",
+ " <td>6</td>\n",
+ " <td>6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Kyrgyzstan</th>\n",
" <th>74.766100</th>\n",
" <th>41.204400</th>\n",
- " <td>44</td>\n",
- " <td>44</td>\n",
+ " <td>58</td>\n",
+ " <td>84</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Laos</th>\n",
" <th>102.495496</th>\n",
" <th>19.856270</th>\n",
- " <td>3</td>\n",
- " <td>6</td>\n",
+ " <td>8</td>\n",
+ " <td>8</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>MS Zaandam</th>\n",
+ " <th>0.000000</th>\n",
+ " <th>0.000000</th>\n",
+ " <td>2</td>\n",
+ " <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Saint Kitts and Nevis</th>\n",
@@ -540,7 +554,7 @@
" <th>-60.978900</th>\n",
" <th>13.909400</th>\n",
" <td>3</td>\n",
- " <td>3</td>\n",
+ " <td>9</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Saint Vincent and the Grenadines</th>\n",
@@ -554,60 +568,64 @@
" <th>38.996815</th>\n",
" <th>34.802075</th>\n",
" <td>5</td>\n",
- " <td>5</td>\n",
+ " <td>9</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Taiwan*</th>\n",
" <th>121.000000</th>\n",
" <th>23.700000</th>\n",
- " <td>235</td>\n",
- " <td>252</td>\n",
+ " <td>283</td>\n",
+ " <td>298</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Venezuela</th>\n",
" <th>-66.589700</th>\n",
" <th>6.423800</th>\n",
- " <td>91</td>\n",
- " <td>107</td>\n",
+ " <td>119</td>\n",
+ " <td>119</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
- " 2020-03-25 00:00:00 \\\n",
+ " 2020-03-28 00:00:00 \\\n",
"Country/Region Long Lat \n",
- "Bahamas -77.396300 25.034300 5 \n",
+ "Bahamas -77.396300 25.034300 10 \n",
+ "Burma 95.956000 21.916200 8 \n",
"Congo (Brazzaville) 21.758700 -4.038300 4 \n",
- "Congo (Kinshasa) 21.758700 -4.038300 48 \n",
+ "Congo (Kinshasa) 21.758700 -4.038300 65 \n",
"Diamond Princess 0.000000 0.000000 712 \n",
"Gambia -15.310100 13.443200 3 \n",
- "Holy See 12.453400 41.902900 4 \n",
- "Kyrgyzstan 74.766100 41.204400 44 \n",
- "Laos 102.495496 19.856270 3 \n",
+ "Holy See 12.453400 41.902900 6 \n",
+ "Kyrgyzstan 74.766100 41.204400 58 \n",
+ "Laos 102.495496 19.856270 8 \n",
+ "MS Zaandam 0.000000 0.000000 2 \n",
"Saint Kitts and Nevis -62.782998 17.357822 2 \n",
"Saint Lucia -60.978900 13.909400 3 \n",
"Saint Vincent and the Grenadines -61.287200 12.984300 1 \n",
"Syria 38.996815 34.802075 5 \n",
- "Taiwan* 121.000000 23.700000 235 \n",
- "Venezuela -66.589700 6.423800 91 \n",
+ "Taiwan* 121.000000 23.700000 283 \n",
+ "Venezuela -66.589700 6.423800 119 \n",
"\n",
- " 2020-03-26 00:00:00 \n",
+ " 2020-03-29 00:00:00 \n",
"Country/Region Long Lat \n",
- "Bahamas -77.396300 25.034300 9 \n",
- "Congo (Brazzaville) 21.758700 -4.038300 4 \n",
- "Congo (Kinshasa) 21.758700 -4.038300 51 \n",
+ "Bahamas -77.396300 25.034300 11 \n",
+ "Burma 95.956000 21.916200 10 \n",
+ "Congo (Brazzaville) 21.758700 -4.038300 19 \n",
+ "Congo (Kinshasa) 21.758700 -4.038300 65 \n",
"Diamond Princess 0.000000 0.000000 712 \n",
- "Gambia -15.310100 13.443200 3 \n",
- "Holy See 12.453400 41.902900 4 \n",
- "Kyrgyzstan 74.766100 41.204400 44 \n",
- "Laos 102.495496 19.856270 6 \n",
+ "Gambia -15.310100 13.443200 4 \n",
+ "Holy See 12.453400 41.902900 6 \n",
+ "Kyrgyzstan 74.766100 41.204400 84 \n",
+ "Laos 102.495496 19.856270 8 \n",
+ "MS Zaandam 0.000000 0.000000 2 \n",
"Saint Kitts and Nevis -62.782998 17.357822 2 \n",
- "Saint Lucia -60.978900 13.909400 3 \n",
+ "Saint Lucia -60.978900 13.909400 9 \n",
"Saint Vincent and the Grenadines -61.287200 12.984300 1 \n",
- "Syria 38.996815 34.802075 5 \n",
- "Taiwan* 121.000000 23.700000 252 \n",
- "Venezuela -66.589700 6.423800 107 "
+ "Syria 38.996815 34.802075 9 \n",
+ "Taiwan* 121.000000 23.700000 298 \n",
+ "Venezuela -66.589700 6.423800 119 "
]
},
"execution_count": 10,
@@ -625,10 +643,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.014167,
- "end_time": "2020-03-27T08:23:24.801950",
+ "duration": 0.011202,
+ "end_time": "2020-03-30T09:42:39.345699",
"exception": false,
- "start_time": "2020-03-27T08:23:24.787783",
+ "start_time": "2020-03-30T09:42:39.334497",
"status": "completed"
},
"tags": []
@@ -642,10 +660,10 @@
"execution_count": 11,
"metadata": {
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@@ -659,10 +677,10 @@
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@@ -676,10 +694,10 @@
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@@ -926,10 +944,10 @@
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@@ -943,10 +961,10 @@
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@@ -971,10 +989,10 @@
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@@ -1007,21 +1025,21 @@
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- "input_path": "/tmp/qa77nd3o/notebooks/process/ToRates.ipynb",
+ "input_path": "notebooks/process/ToRates.ipynb",
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"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/qa77nd3o/notebooks/process/ToRates.ipynb",
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- "geodata_path": "/tmp/qa77nd3o/data/geodata/geo_data.csv",
- "out_folder": "data/covid-19_rates",
- "ts_folder": "/tmp/qa77nd3o/data/covid-19_jhu-csse",
- "wb_path": "/tmp/qa77nd3o/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"
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- "start_time": "2020-03-27T08:23:22.834870",
+ "start_time": "2020-03-30T09:42:37.339971",
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