diff --git a/.renku/workflow/3bae78948a2f4fe59601b86a51a2e7fd_papermill.cwl b/.renku/workflow/3bae78948a2f4fe59601b86a51a2e7fd_papermill.cwl new file mode 100644 index 0000000000000000000000000000000000000000..cb3047326d2726e458e78668a5ae8cd01dc7cd91 --- /dev/null +++ b/.renku/workflow/3bae78948a2f4fe59601b86a51a2e7fd_papermill.cwl @@ -0,0 +1,119 @@ +arguments: [] +baseCommand: +- papermill +class: CommandLineTool +cwlVersion: v1.0 +hints: [] +inputs: + input_1: + default: + class: File + path: ../../notebooks/examples/openzh-covid-19-example.ipynb + inputBinding: + position: 1 + prefix: --report-mode + separate: true + shellQuote: true + streamable: false + type: File + input_2: + default: runs/openzh-covid-19-example.run.ipynb + inputBinding: + position: 2 + separate: true + shellQuote: true + streamable: false + type: string + input_3: + default: save_figures + inputBinding: + position: 3 + prefix: -p + separate: true + shellQuote: true + streamable: false + type: string + input_4: + default: 'True' + inputBinding: + position: 4 + separate: true + shellQuote: true + streamable: false + type: string + input_5: + default: data_path + inputBinding: + position: 5 + prefix: -p + separate: true + shellQuote: true + streamable: false + type: string + input_6: + default: + class: Directory + listing: [] + path: ../../data/openzh-covid-19 + inputBinding: + position: 6 + separate: true + shellQuote: true + streamable: false + type: Directory + input_7: + default: figures_path + inputBinding: + position: 7 + prefix: -p + separate: true + shellQuote: true + streamable: false + type: string + input_8: + default: figures + inputBinding: + position: 8 + separate: true + shellQuote: true + streamable: false + type: string + input_9: + default: + class: File + path: ../../data/ch-population-statistics/ch-population-by-age-canton.xls + streamable: false + type: File +outputs: + output_0: + outputBinding: + glob: $(inputs.input_2) + 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: figures + writable: true + - entry: $(inputs.input_1) + entryname: notebooks/examples/openzh-covid-19-example.ipynb + writable: false + - entry: $(inputs.input_6) + entryname: data/openzh-covid-19 + writable: false + - entry: $(inputs.input_9) + entryname: data/ch-population-statistics/ch-population-by-age-canton.xls + writable: false +successCodes: [] +temporaryFailCodes: [] diff --git a/figures/switzerland-cases-by-canton.html b/figures/switzerland-cases-by-canton.html index ef4d04297d432b93d14835ab72b204ff23e29f80..b594866afb4ba5629428494f236bf54c6c1465ab 100644 --- a/figures/switzerland-cases-by-canton.html +++ 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"papermill": { - "duration": 0.022839, - "end_time": "2020-03-25T08:23:50.694079", + "duration": 0.022429, + "end_time": "2020-03-26T14:06:26.442321", "exception": false, - "start_time": "2020-03-25T08:23:50.671240", + "start_time": "2020-03-26T14:06:26.419892", "status": "completed" }, "tags": [ @@ -72,8 +72,8 @@ "source": [ "# Parameters\n", "save_figures = True\n", - "data_path = \"/tmp/eivltasg/data/openzh-covid-19\"\n", - "figures_path = \"figures\"\n" + "data_path = \"data/openzh-covid-19/\"\n", + "figures_path = \"figures/\"\n" ] }, { @@ -84,10 +84,10 @@ "source_hidden": true }, "papermill": { - "duration": 0.023127, - "end_time": "2020-03-25T08:23:50.731273", + "duration": 0.025987, + "end_time": "2020-03-26T14:06:26.478404", "exception": false, - "start_time": "2020-03-25T08:23:50.708146", + "start_time": "2020-03-26T14:06:26.452417", "status": "completed" }, "tags": [] @@ -108,10 +108,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.00964, - 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"papermill": { - "duration": 0.053372, - "end_time": "2020-03-25T08:24:17.625500", + "duration": 0.065489, + "end_time": "2020-03-26T14:06:51.011198", "exception": false, - "start_time": "2020-03-25T08:24:17.572128", + "start_time": "2020-03-26T14:06:50.945709", "status": "completed" }, "tags": [] @@ -259,7 +259,7 @@ " <td>VS</td>\n", " <td>NaN</td>\n", " <td>1.0</td>\n", - " <td>NaN</td>\n", + " <td>3.0</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", @@ -275,86 +275,86 @@ " </tr>\n", " <tr>\n", " <th>1</th>\n", - " <td>2020-03-03</td>\n", + " <td>2020-02-29</td>\n", " <td>NaN</td>\n", " <td>VS</td>\n", " <td>NaN</td>\n", - " <td>2.0</td>\n", + " <td>1.0</td>\n", + " <td>3.0</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", + " <td>https://www.vs.ch/documents/6756452/7008787/Si...</td>\n", " <td>NaN</td>\n", - " <td>https://vs.ch/documents/529400/6789273/2020+03...</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", - " <td>NaN</td>\n", - " <td>0.581471</td>\n", + " <td>0.290736</td>\n", " <td>NaN</td>\n", " </tr>\n", " <tr>\n", " <th>2</th>\n", - " <td>2020-03-05</td>\n", + " <td>2020-03-01</td>\n", " <td>NaN</td>\n", " <td>VS</td>\n", " <td>NaN</td>\n", - " <td>3.0</td>\n", - " <td>NaN</td>\n", + " <td>2.0</td>\n", + " <td>4.0</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", - " <td>https://www.vs.ch/de/web/coronavirus/info?p_p_...</td>\n", + " <td>https://www.vs.ch/documents/6756452/7008787/Si...</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", - " <td>0.872207</td>\n", + " <td>0.581471</td>\n", " <td>NaN</td>\n", " </tr>\n", " <tr>\n", " <th>3</th>\n", - " <td>2020-03-06</td>\n", + " <td>2020-03-02</td>\n", " <td>NaN</td>\n", " <td>VS</td>\n", " <td>NaN</td>\n", - " <td>5.0</td>\n", - " <td>NaN</td>\n", + " <td>3.0</td>\n", + " <td>4.0</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", - " <td>https://www.vs.ch/de/web/coronavirus/info?p_p_...</td>\n", + " <td>https://www.vs.ch/documents/6756452/7008787/Si...</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", - " <td>1.453679</td>\n", + " <td>0.872207</td>\n", " <td>NaN</td>\n", " </tr>\n", " <tr>\n", " <th>4</th>\n", - " <td>2020-03-08</td>\n", + " <td>2020-03-03</td>\n", " <td>NaN</td>\n", " <td>VS</td>\n", " <td>NaN</td>\n", - " <td>7.0</td>\n", - " <td>NaN</td>\n", + " <td>3.0</td>\n", + " <td>5.0</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", - " <td>https://www.vs.ch/de/web/coronavirus/info?p_p_...</td>\n", + " <td>https://vs.ch/documents/529400/6789273/2020+03...</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", " <td>NaN</td>\n", - " <td>2.035150</td>\n", + " <td>0.872207</td>\n", " <td>NaN</td>\n", " </tr>\n", " </tbody>\n", @@ -364,24 +364,24 @@ 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NaN \n", - "1 https://vs.ch/documents/529400/6789273/2020+03... NaN \n", - "2 https://www.vs.ch/de/web/coronavirus/info?p_p_... NaN \n", - "3 https://www.vs.ch/de/web/coronavirus/info?p_p_... NaN \n", - "4 https://www.vs.ch/de/web/coronavirus/info?p_p_... NaN \n", + "1 https://www.vs.ch/documents/6756452/7008787/Si... NaN \n", + "2 https://www.vs.ch/documents/6756452/7008787/Si... NaN \n", + "3 https://www.vs.ch/documents/6756452/7008787/Si... NaN \n", + "4 https://vs.ch/documents/529400/6789273/2020+03... NaN \n", "\n", " ncumul_ICU_intub ncumul_deceased_suspect TotalPosTests1 TotalCured \\\n", "0 NaN NaN NaN NaN \n", @@ -392,10 +392,10 @@ "\n", " ncumul_conf_100k ncumul_deceased_100k \n", "0 0.290736 NaN \n", - "1 0.581471 NaN \n", - "2 0.872207 NaN \n", - "3 1.453679 NaN \n", - "4 2.035150 NaN " + "1 0.290736 NaN \n", + "2 0.581471 NaN \n", + "3 0.872207 NaN \n", + "4 0.872207 NaN " ] }, "execution_count": 7, @@ -412,10 +412,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.010304, - "end_time": "2020-03-25T08:24:17.647569", + "duration": 0.010133, + "end_time": "2020-03-26T14:06:51.040474", "exception": false, - "start_time": "2020-03-25T08:24:17.637265", + "start_time": "2020-03-26T14:06:51.030341", "status": "completed" }, "tags": [] @@ -434,10 +434,10 @@ "source_hidden": true }, "papermill": { - "duration": 0.028492, - "end_time": "2020-03-25T08:24:17.686440", + "duration": 0.033181, + "end_time": "2020-03-26T14:06:51.082278", "exception": false, - 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