diff --git a/.renku/workflow/0a2b3c5a9a6e43f3a9b2b28d796ddb2e_papermill.cwl b/.renku/workflow/0a2b3c5a9a6e43f3a9b2b28d796ddb2e_papermill.cwl new file mode 100644 index 0000000000000000000000000000000000000000..ac5dcec74727923aeddcc8d3e6448b3a1badebf3 --- /dev/null +++ b/.renku/workflow/0a2b3c5a9a6e43f3a9b2b28d796ddb2e_papermill.cwl @@ -0,0 +1,114 @@ +arguments: [] +baseCommand: +- papermill +class: CommandLineTool +cwlVersion: v1.0 +hints: [] +inputs: + input_1: + default: + class: File + path: ../../notebooks/datasets_summary.ipynb + inputBinding: + position: 1 + separate: true + shellQuote: true + streamable: false + type: File + input_2: + default: runs/dataset_summary.run.ipynb + inputBinding: + position: 2 + separate: true + shellQuote: true + streamable: false + type: string + input_3: + default: data_path + inputBinding: + position: 3 + prefix: -p + separate: true + shellQuote: true + streamable: false + type: string + input_4: + default: + class: Directory + listing: [] + path: ../../data + inputBinding: + position: 4 + separate: true + shellQuote: true + streamable: false + type: Directory + input_5: + default: + class: File + path: ../../data/covid-19-italy/dpc-covid19-ita-regioni.csv + streamable: false + type: File + input_6: + default: + class: Directory + listing: [] + path: ../../data/atlas + streamable: false + type: Directory + input_7: + default: + class: File + path: ../../data/covid-19-us-nyt/us-counties.csv + streamable: false + type: File + input_8: + default: + class: Directory + listing: [] + path: ../../data/covid-19-spain + streamable: false + type: Directory + input_9: + default: + class: File + path: ../../data/covid-19-ecdc/covid-19-ecdc.csv + streamable: false + type: File +outputs: + output_0: + outputBinding: + glob: $(inputs.input_2) + streamable: false + type: File +permanentFailCodes: [] +requirements: +- class: InlineJavascriptRequirement +- class: InitialWorkDirRequirement + listing: + - entry: '$({"listing": [], "class": "Directory"})' + entryname: runs + writable: true + - entry: $(inputs.input_1) + entryname: notebooks/datasets_summary.ipynb + writable: false + - entry: $(inputs.input_4) + entryname: data + writable: false + - entry: $(inputs.input_5) + entryname: data/covid-19-italy/dpc-covid19-ita-regioni.csv + writable: false + - entry: $(inputs.input_6) + entryname: data/atlas + writable: false + - entry: $(inputs.input_7) + entryname: data/covid-19-us-nyt/us-counties.csv + writable: false + - entry: $(inputs.input_8) + entryname: data/covid-19-spain + writable: false + - entry: $(inputs.input_9) + entryname: data/covid-19-ecdc/covid-19-ecdc.csv + writable: false +successCodes: [] +temporaryFailCodes: [] diff --git a/runs/dataset_summary.run.ipynb b/runs/dataset_summary.run.ipynb index 6a00d77cdef53ecc583032a3fbbc5f3063a5ccea..92264feb8f7ca5b02279adf6baa490083910c396 100644 --- a/runs/dataset_summary.run.ipynb +++ b/runs/dataset_summary.run.ipynb @@ -5,10 +5,10 @@ "execution_count": 1, "metadata": { "papermill": { - "duration": 0.063933, - "end_time": "2020-04-28T19:27:53.765279", + "duration": 0.06638, + "end_time": "2020-05-25T12:00:49.632603", "exception": false, - "start_time": "2020-04-28T19:27:53.701346", + "start_time": "2020-05-25T12:00:49.566223", "status": "completed" }, "tags": [] @@ -24,10 +24,10 @@ "execution_count": 2, "metadata": { "papermill": { - "duration": 0.048917, - "end_time": "2020-04-28T19:27:53.836867", + "duration": 0.045254, + "end_time": "2020-05-25T12:00:49.701957", "exception": false, - "start_time": "2020-04-28T19:27:53.787950", + "start_time": "2020-05-25T12:00:49.656703", "status": "completed" }, "tags": [] @@ -61,10 +61,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.009844, - "end_time": "2020-04-28T19:27:53.856840", + "duration": 0.011931, + "end_time": "2020-05-25T12:00:49.731945", "exception": false, - "start_time": "2020-04-28T19:27:53.846996", + "start_time": "2020-05-25T12:00:49.720014", "status": "completed" }, "tags": [] @@ -82,10 +82,10 @@ "execution_count": 3, "metadata": { "papermill": { - "duration": 0.448861, - "end_time": "2020-04-28T19:27:54.316818", + "duration": 0.51998, + "end_time": "2020-05-25T12:00:50.262074", "exception": false, - "start_time": "2020-04-28T19:27:53.867957", + "start_time": "2020-05-25T12:00:49.742094", "status": "completed" }, "tags": [] @@ -105,10 +105,10 @@ "execution_count": 4, "metadata": { "papermill": { - "duration": 0.055302, - "end_time": "2020-04-28T19:27:54.398557", + "duration": 0.050635, + "end_time": "2020-05-25T12:00:50.335250", "exception": false, - "start_time": "2020-04-28T19:27:54.343255", + "start_time": "2020-05-25T12:00:50.284615", "status": "completed" }, "tags": [] @@ -125,10 +125,10 @@ "execution_count": 5, "metadata": { "papermill": { - "duration": 0.039177, - "end_time": "2020-04-28T19:27:54.456336", + "duration": 0.043799, + "end_time": "2020-05-25T12:00:50.400048", "exception": false, - "start_time": "2020-04-28T19:27:54.417159", + "start_time": "2020-05-25T12:00:50.356249", "status": "completed" }, "tags": [ @@ -137,8 +137,7 @@ }, "outputs": [], "source": [ - "data_path = \"../data\"\n", - "atlas_path = \"../data/atlas\"" + "data_path = \"../data\"" ] }, { @@ -146,10 +145,10 @@ "execution_count": 6, "metadata": { "papermill": { - "duration": 0.047617, - "end_time": "2020-04-28T19:27:54.523422", + "duration": 0.040278, + "end_time": "2020-05-25T12:00:50.459195", "exception": false, - "start_time": "2020-04-28T19:27:54.475805", + "start_time": "2020-05-25T12:00:50.418917", "status": "completed" }, "tags": [ @@ -159,8 +158,7 @@ "outputs": [], "source": [ "# Parameters\n", - "data_path = \"data/\"\n", - "atlas_path = \"data/atlas/\"\n" + "data_path = \"data/\"\n" ] }, { @@ -168,10 +166,10 @@ "execution_count": 7, "metadata": { "papermill": { - "duration": 0.047258, - "end_time": "2020-04-28T19:27:54.587783", + "duration": 0.043025, + "end_time": "2020-05-25T12:00:50.521118", "exception": false, - "start_time": "2020-04-28T19:27:54.540525", + "start_time": "2020-05-25T12:00:50.478093", "status": "completed" }, "tags": [] @@ -180,6 +178,7 @@ "source": [ "# Instantiating the CaseConverter to read in the data.\n", "# It takes a path to the atlas dataset as an argument - the atlas holds various population and country metadata data. \n", + "atlas_path = Path(data_path) / \"atlas\"\n", "converter = CaseConverter(atlas_path)" ] }, @@ -187,10 +186,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.01167, - "end_time": "2020-04-28T19:27:54.622339", + "duration": 0.010508, + "end_time": "2020-05-25T12:00:50.550686", "exception": false, - "start_time": "2020-04-28T19:27:54.610669", + "start_time": "2020-05-25T12:00:50.540178", "status": "completed" }, "tags": [] @@ -206,10 +205,10 @@ "execution_count": 8, "metadata": { "papermill": { - "duration": 0.356898, - "end_time": "2020-04-28T19:27:54.989486", + "duration": 0.438231, + "end_time": 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"2020-05-25T12:00:51.228603", "exception": false, - "start_time": "2020-04-28T19:27:55.182011", + "start_time": "2020-05-25T12:00:51.175254", "status": "completed" }, "tags": [] @@ -406,10 +405,10 @@ "execution_count": 11, "metadata": { "papermill": { - "duration": 0.074552, - "end_time": "2020-04-28T19:27:55.354194", + "duration": 0.078398, + "end_time": "2020-05-25T12:00:51.332446", "exception": false, - "start_time": "2020-04-28T19:27:55.279642", + "start_time": "2020-05-25T12:00:51.254048", "status": "completed" }, "tags": [] @@ -447,82 +446,82 @@ " <tr>\n", " <th>0</th>\n", " <td>United States of America</td>\n", - " <td>53189</td>\n", - " <td>16.257425</td>\n", - " <td>939053</td>\n", - " <td>287.025206</td>\n", + " <td>56245</td>\n", + " <td>17.191503</td>\n", + " <td>988451</td>\n", + " <td>302.123897</td>\n", " </tr>\n", " <tr>\n", " <th>1</th>\n", " <td>Italy</td>\n", - " <td>26384</td>\n", - " <td>43.659507</td>\n", - " <td>195351</td>\n", - " <td>323.261381</td>\n", + " <td>26977</td>\n", + " <td>44.640786</td>\n", + " <td>199414</td>\n", + " <td>329.984720</td>\n", " </tr>\n", " <tr>\n", " <th>2</th>\n", " <td>France</td>\n", - " <td>22614</td>\n", - " <td>33.758666</td>\n", - " <td>124114</td>\n", - " <td>185.280051</td>\n", + " <td>23293</td>\n", + " <td>34.772292</td>\n", + " <td>128339</td>\n", + " <td>191.587222</td>\n", " </tr>\n", " <tr>\n", " <th>3</th>\n", " <td>United Kingdom</td>\n", - " <td>20319</td>\n", - " <td>30.559946</td>\n", - " <td>148377</td>\n", - " <td>223.160252</td>\n", + " <td>21092</td>\n", + " <td>31.722545</td>\n", + " <td>157149</td>\n", + " <td>236.353414</td>\n", " </tr>\n", " <tr>\n", " <th>4</th>\n", " <td>Belgium</td>\n", - " <td>6917</td>\n", - " <td>60.558211</td>\n", - " <td>45325</td>\n", - " <td>396.819560</td>\n", + " <td>7207</td>\n", + " <td>63.097155</td>\n", + " <td>46687</td>\n", + " <td>408.743846</td>\n", " </tr>\n", " <tr>\n", " <th>5</th>\n", - " <td>Iran</td>\n", - " <td>5650</td>\n", - " <td>6.907068</td>\n", - " <td>89328</td>\n", - " <td>109.202575</td>\n", + " <td>Germany</td>\n", + " <td>5913</td>\n", + " <td>7.130288</td>\n", + " <td>156337</td>\n", + " <td>188.521545</td>\n", " </tr>\n", " <tr>\n", " <th>6</th>\n", - " <td>Germany</td>\n", - " <td>5640</td>\n", - " <td>6.801087</td>\n", - " <td>154175</td>\n", - " <td>185.914462</td>\n", + " <td>Iran</td>\n", + " <td>5806</td>\n", + " <td>7.097776</td>\n", + " <td>91472</td>\n", + " <td>111.823593</td>\n", " </tr>\n", " <tr>\n", " <th>7</th>\n", " <td>China</td>\n", - " <td>4636</td>\n", - " <td>0.332871</td>\n", - " <td>83909</td>\n", - " <td>6.024786</td>\n", + " <td>4637</td>\n", + " <td>0.332943</td>\n", + " <td>83938</td>\n", + " <td>6.026868</td>\n", " </tr>\n", " <tr>\n", " <th>8</th>\n", - " <td>Netherlands</td>\n", - " <td>4409</td>\n", - " <td>25.587578</td>\n", - " <td>37190</td>\n", - " <td>215.831718</td>\n", + " <td>Brazil</td>\n", + " <td>4543</td>\n", + " <td>2.168814</td>\n", + " <td>66501</td>\n", + " <td>31.747368</td>\n", " </tr>\n", " <tr>\n", " <th>9</th>\n", - " <td>Brazil</td>\n", - " <td>4016</td>\n", - " <td>1.917226</td>\n", - " <td>58509</td>\n", - " <td>27.932012</td>\n", + " <td>Netherlands</td>\n", + " <td>4518</td>\n", + " <td>26.220159</td>\n", + " <td>38245</td>\n", + " <td>221.954398</td>\n", " </tr>\n", " </tbody>\n", "</table>\n", @@ -530,28 +529,28 @@ ], "text/plain": [ " Country Deaths Deaths per 100k Positive cases \\\n", - "0 United States of America 53189 16.257425 939053 \n", - "1 Italy 26384 43.659507 195351 \n", - "2 France 22614 33.758666 124114 \n", - "3 United Kingdom 20319 30.559946 148377 \n", - "4 Belgium 6917 60.558211 45325 \n", - "5 Iran 5650 6.907068 89328 \n", - "6 Germany 5640 6.801087 154175 \n", - "7 China 4636 0.332871 83909 \n", - "8 Netherlands 4409 25.587578 37190 \n", - "9 Brazil 4016 1.917226 58509 \n", + "0 United States of America 56245 17.191503 988451 \n", + "1 Italy 26977 44.640786 199414 \n", + "2 France 23293 34.772292 128339 \n", + "3 United Kingdom 21092 31.722545 157149 \n", + "4 Belgium 7207 63.097155 46687 \n", + "5 Germany 5913 7.130288 156337 \n", + "6 Iran 5806 7.097776 91472 \n", + "7 China 4637 0.332943 83938 \n", + "8 Brazil 4543 2.168814 66501 \n", + "9 Netherlands 4518 26.220159 38245 \n", "\n", " Positive cases per 100k \n", - "0 287.025206 \n", - "1 323.261381 \n", - "2 185.280051 \n", - "3 223.160252 \n", - "4 396.819560 \n", - "5 109.202575 \n", - "6 185.914462 \n", - "7 6.024786 \n", - "8 215.831718 \n", - "9 27.932012 " + "0 302.123897 \n", + "1 329.984720 \n", + "2 191.587222 \n", + "3 236.353414 \n", + "4 408.743846 \n", + "5 188.521545 \n", + "6 111.823593 \n", + "7 6.026868 \n", + "8 31.747368 \n", + "9 221.954398 " ] }, "execution_count": 11, @@ -589,10 +588,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.011835, - "end_time": "2020-04-28T19:27:55.388505", + "duration": 0.013571, + "end_time": "2020-05-25T12:00:51.370525", "exception": false, - "start_time": "2020-04-28T19:27:55.376670", + "start_time": "2020-05-25T12:00:51.356954", "status": "completed" }, "tags": [] @@ -608,10 +607,10 @@ "execution_count": 12, "metadata": { "papermill": { - "duration": 2.911695, - "end_time": "2020-04-28T19:27:58.312325", + "duration": 5.605204, + "end_time": "2020-05-25T12:00:56.989133", "exception": false, - "start_time": "2020-04-28T19:27:55.400630", + "start_time": "2020-05-25T12:00:51.383929", "status": "completed" }, "tags": [] @@ -632,10 +631,10 @@ "execution_count": 13, "metadata": { "papermill": { - "duration": 0.057327, - "end_time": "2020-04-28T19:27:58.414073", + "duration": 0.035459, + "end_time": "2020-05-25T12:00:57.049068", "exception": false, - "start_time": "2020-04-28T19:27:58.356746", + "start_time": "2020-05-25T12:00:57.013609", "status": "completed" }, "tags": [] @@ -652,10 +651,10 @@ "execution_count": 14, "metadata": { "papermill": { - "duration": 0.067214, - "end_time": "2020-04-28T19:27:58.513312", + "duration": 0.04504, + "end_time": "2020-05-25T12:00:57.111435", "exception": false, - "start_time": "2020-04-28T19:27:58.446098", + "start_time": "2020-05-25T12:00:57.066395", "status": "completed" }, "tags": [] @@ -674,10 +673,10 @@ "execution_count": 15, "metadata": { "papermill": { - "duration": 0.187103, - "end_time": "2020-04-28T19:27:58.725007", + "duration": 0.209453, + "end_time": "2020-05-25T12:00:57.344621", "exception": false, - "start_time": "2020-04-28T19:27:58.537904", + "start_time": "2020-05-25T12:00:57.135168", "status": "completed" }, "tags": [] @@ -704,7 +703,7 @@ "text/html": [ "\n", " <h4>United States</h4>\n", - " <p style=\"font-size: smaller\">(based on data from Apr. 25, 2020)</p>\n", + " <p style=\"font-size: smaller\">(based on data from May. 23, 2020)</p>\n", " <table border=\"1\" class=\"dataframe\">\n", " <thead>\n", " <tr style=\"text-align: right;\">\n", @@ -718,44 +717,44 @@ " <tbody>\n", " <tr>\n", " <td>New York City, New York</td>\n", - " <td>11419</td>\n", - " <td>136.970741</td>\n", - " <td>155124</td>\n", - " <td>1860.710149</td>\n", + " <td>20621</td>\n", + " <td>247.348598</td>\n", + " <td>202062</td>\n", + " <td>2423.730784</td>\n", " </tr>\n", " <tr>\n", - " <td>Nassau, New York</td>\n", - " <td>1917</td>\n", - " <td>141.275414</td>\n", - " <td>33798</td>\n", - " <td>2490.780619</td>\n", + " <td>Cook, Illinois</td>\n", + " <td>3246</td>\n", + " <td>63.026275</td>\n", + " <td>70417</td>\n", + " <td>1367.258530</td>\n", " </tr>\n", " <tr>\n", - " <td>Wayne, Michigan</td>\n", - " <td>1560</td>\n", - " <td>89.176336</td>\n", - " <td>15548</td>\n", - " <td>888.790820</td>\n", + " <td>Nassau, New York</td>\n", + " <td>2578</td>\n", + " <td>189.988533</td>\n", + " <td>39726</td>\n", + " <td>2927.651070</td>\n", " </tr>\n", " <tr>\n", - " <td>Cook, Illinois</td>\n", - " <td>1267</td>\n", - " <td>24.600829</td>\n", - " <td>29058</td>\n", - " <td>564.207483</td>\n", + " <td>Wayne, Michigan</td>\n", + " <td>2361</td>\n", + " <td>134.964955</td>\n", + " <td>19697</td>\n", + " <td>1125.965577</td>\n", " </tr>\n", " <tr>\n", - " <td>Suffolk, New York</td>\n", - " <td>1085</td>\n", - " <td>73.479566</td>\n", - " <td>31368</td>\n", - " <td>2124.338261</td>\n", + " <td>Los Angeles, California</td>\n", + " <td>2090</td>\n", + " <td>20.818585</td>\n", + " <td>44055</td>\n", + " <td>438.833852</td>\n", " </tr>\n", " </tbody>\n", "</table>\n", "\n", " <h4>Spain</h4>\n", - " <p style=\"font-size: smaller\">(based on data from Apr. 26, 2020)</p>\n", + " <p style=\"font-size: smaller\">(based on data from May. 24, 2020)</p>\n", " <table border=\"1\" class=\"dataframe\">\n", " <thead>\n", " <tr style=\"text-align: right;\">\n", @@ -769,44 +768,44 @@ " <tbody>\n", " <tr>\n", " <td>Madrid</td>\n", - " <td>7922.0</td>\n", - " <td>118.914150</td>\n", - " <td>62817</td>\n", - " <td>942.922259</td>\n", + " <td>8977.0</td>\n", + " <td>134.750356</td>\n", + " <td>72342.0</td>\n", + " <td>1085.898436</td>\n", " </tr>\n", " <tr>\n", " <td>Cataluña</td>\n", - " <td>4566.0</td>\n", - " <td>59.925239</td>\n", - " <td>47838</td>\n", - " <td>627.836967</td>\n", - " </tr>\n", - " <tr>\n", - " <td>Castilla-La Mancha</td>\n", - " <td>2330.0</td>\n", - " <td>110.618891</td>\n", - " <td>18995</td>\n", - " <td>901.805082</td>\n", + " <td>6701.0</td>\n", + " <td>87.945472</td>\n", + " <td>57531.0</td>\n", + " <td>755.050139</td>\n", " </tr>\n", " <tr>\n", " <td>Castilla y León</td>\n", - " <td>1666.0</td>\n", - " <td>68.880148</td>\n", - " <td>18684</td>\n", - " <td>772.483001</td>\n", + " <td>1961.0</td>\n", + " <td>81.076813</td>\n", + " <td>24918.0</td>\n", + " <td>1030.225403</td>\n", " </tr>\n", " <tr>\n", " <td>PaÃs Vasco</td>\n", - " <td>1230.0</td>\n", - " <td>56.741986</td>\n", - " <td>14315</td>\n", - " <td>660.375226</td>\n", + " <td>1494.0</td>\n", + " <td>68.920754</td>\n", + " <td>18779.0</td>\n", + " <td>866.307116</td>\n", + " </tr>\n", + " <tr>\n", + " <td>C. Valenciana</td>\n", + " <td>1393.0</td>\n", + " <td>27.839015</td>\n", + " <td>14797.0</td>\n", + " <td>295.717088</td>\n", " </tr>\n", " </tbody>\n", "</table>\n", "\n", " <h4>Italy</h4>\n", - " <p style=\"font-size: smaller\">(based on data from Apr. 26, 2020)</p>\n", + " <p style=\"font-size: smaller\">(based on data from May. 24, 2020)</p>\n", " <table border=\"1\" class=\"dataframe\">\n", " <thead>\n", " <tr style=\"text-align: right;\">\n", @@ -820,38 +819,38 @@ " <tbody>\n", " <tr>\n", " <td>Lombardy</td>\n", - " <td>13325</td>\n", - " <td>132.356672</td>\n", - " <td>72889</td>\n", - " <td>724.003411</td>\n", + " <td>15840</td>\n", + " <td>157.338062</td>\n", + " <td>87110</td>\n", + " <td>865.260014</td>\n", " </tr>\n", " <tr>\n", " <td>Emilia-Romagna</td>\n", - " <td>3386</td>\n", - " <td>75.928186</td>\n", - " <td>24450</td>\n", - " <td>548.270571</td>\n", + " <td>4055</td>\n", + " <td>90.929945</td>\n", + " <td>27558</td>\n", + " <td>617.964842</td>\n", " </tr>\n", " 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