diff --git a/.renku/workflow/fa727a9ee40f49c7babf6113952d17d8.cwl b/.renku/workflow/fa727a9ee40f49c7babf6113952d17d8.cwl new file mode 100644 index 0000000000000000000000000000000000000000..ded5af8d335234e84b7c639271cf5c3dd28a75b7 --- /dev/null +++ b/.renku/workflow/fa727a9ee40f49c7babf6113952d17d8.cwl @@ -0,0 +1,182 @@ +class: Workflow +cwlVersion: v1.0 +hints: [] +inputs: + input_1: + default: + class: File + path: ../../notebooks/examples/italy-covid-19.ipynb + streamable: false + type: File + input_10: + default: + class: File + path: ../../notebooks/openzh-covid-19-dashboard.ipynb + streamable: false + type: File + input_11: + default: runs/openzh-covid-19-dashboard.run.ipynb + streamable: false + type: string + input_12: + default: data_path + streamable: false + type: string + input_13: + default: + class: Directory + listing: [] + path: ../../data/openzh-covid-19 + streamable: false + type: Directory + input_14: + default: + class: File + path: ../../data/ch-population-statistics/ch-population-by-age-canton.xls + streamable: false + type: File + input_15: + default: ts_folder + streamable: false + type: string + input_16: + default: + class: Directory + listing: [] + path: ../../data/covid-19_jhu-csse + streamable: false + type: Directory + input_17: + default: rates_folder + streamable: false + type: string + input_18: + default: + class: Directory + listing: [] + path: ../../data/covid-19_rates + streamable: false + type: Directory + input_19: + default: geodata_path + streamable: false + type: string + input_2: + default: runs/italy-covid-19.ipynb + streamable: false + type: string + input_20: + default: + class: File + path: ../../data/geodata/geo_data.csv + streamable: false + type: File + input_21: + default: + class: File + path: ../../notebooks/Dashboard.ipynb + streamable: false + type: File + input_22: + default: runs/Dashboard.run.ipynb + streamable: false + type: string + input_3: + default: data_folder + streamable: false + type: string + input_4: + default: + class: Directory + listing: [] + path: ../../data/covid-19-italy + streamable: false + type: Directory + input_5: + default: + class: File + path: ../../notebooks/covidtracking-dashboard.ipynb + streamable: false + type: File + input_6: + default: runs/covidtracking-dashboard.ipynb + streamable: false + type: string + input_7: + default: data_path + streamable: false + type: string + input_8: + default: + class: Directory + listing: [] + path: ../../data/covidtracking + streamable: false + type: Directory + input_9: + default: + class: File + path: ../../data/geodata/us_pop_fung_2019.csv + streamable: false + type: File +outputs: + output_0: + outputSource: step_3/output_0 + streamable: false + type: File + output_1: + outputSource: step_1/output_0 + streamable: false + type: File + output_2: + outputSource: step_2/output_0 + streamable: false + type: File + output_3: + outputSource: step_4/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 + out: + - output_0 + run: f2c255fbcb87444ea80501341f0b7f1a_papermill.cwl + step_2: + in: + input_1: input_5 + input_2: input_6 + input_3: input_7 + input_4: input_8 + input_5: input_9 + out: + - output_0 + run: 30e7c6a1fdb74ccea2652434f5c83d13_papermill.cwl + step_3: + in: + input_1: input_10 + input_2: input_11 + input_3: input_12 + input_4: input_13 + input_5: input_14 + out: + - output_0 + run: 0415b23203ef422185f0ecf77290cbd3_papermill.cwl + step_4: + in: + input_2: input_15 + input_3: input_16 + input_4: input_17 + input_5: input_18 + input_6: input_19 + input_7: input_20 + input_8: input_21 + input_9: input_22 + out: + - output_0 + run: c57735c62b424192b938f9538b4d65c0_papermill.cwl diff --git a/runs/Dashboard.run.ipynb b/runs/Dashboard.run.ipynb index f50d287e2754af664654ed38f72f4a613002b133..10c70b83ed6fb9d6e96c0673c88faa0d0c13a8dc 100644 --- a/runs/Dashboard.run.ipynb +++ b/runs/Dashboard.run.ipynb @@ -8,10 +8,10 @@ "source_hidden": true }, "papermill": { - "duration": 0.528766, - "end_time": "2020-04-07T07:26:27.857469", + "duration": 0.495147, + "end_time": "2020-04-08T07:28:15.728994", "exception": false, - "start_time": "2020-04-07T07:26:27.328703", + "start_time": "2020-04-08T07:28:15.233847", "status": "completed" }, "tags": [] @@ -33,10 +33,10 @@ "source_hidden": true }, "papermill": { - "duration": 0.02378, - "end_time": "2020-04-07T07:26:27.898514", + "duration": 0.032585, + "end_time": "2020-04-08T07:28:15.781157", "exception": false, - "start_time": "2020-04-07T07:26:27.874734", + "start_time": "2020-04-08T07:28:15.748572", "status": "completed" }, "tags": [ @@ -60,10 +60,10 @@ "source_hidden": true }, "papermill": { - "duration": 0.031283, - "end_time": "2020-04-07T07:26:27.952574", + "duration": 0.028606, + "end_time": "2020-04-08T07:28:15.832313", "exception": false, - "start_time": "2020-04-07T07:26:27.921291", + "start_time": "2020-04-08T07:28:15.803707", "status": "completed" }, "tags": [ @@ -73,11 +73,11 @@ "outputs": [], "source": [ "# Parameters\n", - "PAPERMILL_INPUT_PATH = \"/tmp/jtazphdl/notebooks/Dashboard.ipynb\"\n", + "PAPERMILL_INPUT_PATH = \"/tmp/lik815p7/notebooks/Dashboard.ipynb\"\n", "PAPERMILL_OUTPUT_PATH = \"runs/Dashboard.run.ipynb\"\n", - "ts_folder = \"/tmp/jtazphdl/data/covid-19_jhu-csse\"\n", - "rates_folder = \"/tmp/jtazphdl/data/covid-19_rates\"\n", - "geodata_path = \"/tmp/jtazphdl/data/geodata/geo_data.csv\"\n" + "ts_folder = \"/tmp/lik815p7/data/covid-19_jhu-csse\"\n", + "rates_folder = \"/tmp/lik815p7/data/covid-19_rates\"\n", + "geodata_path = \"/tmp/lik815p7/data/geodata/geo_data.csv\"\n" ] }, { @@ -88,10 +88,10 @@ "source_hidden": true }, "papermill": { - "duration": 0.022198, - "end_time": "2020-04-07T07:26:27.988402", + "duration": 0.0243, + "end_time": "2020-04-08T07:28:15.873912", "exception": false, - "start_time": "2020-04-07T07:26:27.966204", + "start_time": "2020-04-08T07:28:15.849612", "status": "completed" }, "tags": [] @@ -109,10 +109,10 @@ "source_hidden": true }, "papermill": { - "duration": 0.116549, - "end_time": "2020-04-07T07:26:28.118504", + "duration": 0.199694, + "end_time": "2020-04-08T07:28:16.086781", "exception": false, - "start_time": "2020-04-07T07:26:28.001955", + "start_time": "2020-04-08T07:28:15.887087", "status": "completed" }, "tags": [] @@ -133,10 +133,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.01313, - "end_time": "2020-04-07T07:26:28.149878", + "duration": 0.013364, + "end_time": "2020-04-08T07:28:16.128826", "exception": false, - "start_time": "2020-04-07T07:26:28.136748", + "start_time": "2020-04-08T07:28:16.115462", "status": "completed" }, "tags": [] @@ -157,10 +157,10 @@ "source_hidden": true }, "papermill": { - "duration": 0.041614, - "end_time": "2020-04-07T07:26:28.204754", + "duration": 0.049799, + "end_time": "2020-04-08T07:28:16.190287", "exception": false, - "start_time": "2020-04-07T07:26:28.163140", + "start_time": "2020-04-08T07:28:16.140488", "status": "completed" }, "tags": [] @@ -169,7 +169,7 @@ { "data": { "text/html": [ - "<em>Data up to Apr 06 2020; countries with 100 or more confirmed cases.</em>" + "<em>Data up to Apr 07 2020; countries with 100 or more confirmed cases.</em>" ], "text/plain": [ "<IPython.core.display.HTML object>" @@ -188,10 +188,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.013707, - "end_time": "2020-04-07T07:26:28.238763", + "duration": 0.012856, + "end_time": "2020-04-08T07:28:16.225352", "exception": false, - "start_time": "2020-04-07T07:26:28.225056", + "start_time": "2020-04-08T07:28:16.212496", "status": "completed" }, "tags": [] @@ -208,10 +208,10 @@ "source_hidden": true }, "papermill": { - "duration": 0.024507, - "end_time": "2020-04-07T07:26:28.278121", + "duration": 0.028943, + "end_time": "2020-04-08T07:28:16.266855", "exception": false, - "start_time": "2020-04-07T07:26:28.253614", + "start_time": "2020-04-08T07:28:16.237912", "status": "completed" }, "tags": [] @@ -229,10 +229,10 @@ "source_hidden": true }, "papermill": { - "duration": 0.050457, - "end_time": "2020-04-07T07:26:28.345223", + "duration": 0.056671, + "end_time": "2020-04-08T07:28:16.346929", "exception": false, - "start_time": "2020-04-07T07:26:28.294766", + "start_time": "2020-04-08T07:28:16.290258", "status": "completed" }, "tags": [] @@ -250,10 +250,10 @@ "source_hidden": true }, "papermill": { - "duration": 0.119031, - "end_time": "2020-04-07T07:26:28.484016", + "duration": 0.117031, + "end_time": "2020-04-08T07:28:16.488599", "exception": false, - "start_time": "2020-04-07T07:26:28.364985", + "start_time": "2020-04-08T07:28:16.371568", "status": "completed" }, "tags": [] @@ -263,10 +263,10 @@ "data": { "text/html": [ "\n", - "<div id=\"altair-viz-ae3b031295154667afe24a394e0da6db\"></div>\n", + "<div id=\"altair-viz-89c7f1ff46784939bc818312f9c782a6\"></div>\n", "<script type=\"text/javascript\">\n", " (function(spec, embedOpt){\n", - " const outputDiv = document.getElementById(\"altair-viz-ae3b031295154667afe24a394e0da6db\");\n", + " const outputDiv = document.getElementById(\"altair-viz-89c7f1ff46784939bc818312f9c782a6\");\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", @@ -307,7 +307,7 @@ " .catch(showError)\n", " .then(() => displayChart(vegaEmbed));\n", " }\n", - " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300, \"stroke\": null}}, \"layer\": [{\"data\": {\"sphere\": true}, \"mark\": {\"type\": \"geoshape\", \"fill\": \"#cae6ef\"}}, {\"data\": {\"graticule\": true}, \"mark\": {\"type\": \"geoshape\", \"stroke\": \"white\", \"strokeWidth\": 0.5}}, {\"data\": {\"url\": \"https://vega.github.io/vega-datasets/data/world-110m.json\", 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\"Deaths/100k\": 0.0400044725000255, \"Confirmed\": 467.0, \"Deaths\": 2.0, \"Long\": -84.19208768, \"Lat\": 9.97634464}, {\"Country/Region\": \"Cote d'Ivoire\", \"Confirmed/100k\": 1.2884321252959157, \"Deaths/100k\": 0.011966861844853708, \"Confirmed\": 323.0, \"Deaths\": 3.0, \"Long\": -5.5692157, \"Lat\": 7.6284262}, {\"Country/Region\": \"Croatia\", \"Confirmed/100k\": 29.882134298430085, \"Deaths/100k\": 0.39125544089597497, \"Confirmed\": 1222.0, \"Deaths\": 16.0, \"Long\": 16.40412899, \"Lat\": 45.08047631}, {\"Country/Region\": \"Cuba\", \"Confirmed/100k\": 3.0869266188151876, \"Deaths/100k\": 0.0793781130552477, \"Confirmed\": 350.0, \"Deaths\": 9.0, \"Long\": -79.01605384, \"Lat\": 21.62289528}, {\"Country/Region\": \"Cyprus\", \"Confirmed/100k\": 39.09978011629031, \"Deaths/100k\": 0.7567699377346512, \"Confirmed\": 465.0, \"Deaths\": 9.0, \"Long\": 33.0060022, \"Lat\": 34.91667211}, {\"Country/Region\": \"Czechia\", \"Confirmed/100k\": 45.38056098918706, \"Deaths/100k\": 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{ - "duration": 6.349341, - "end_time": "2020-04-07T07:26:32.841158", + "duration": 6.263084, + "end_time": "2020-04-08T07:28:20.732737", "environment_variables": {}, "exception": null, - "input_path": "/tmp/jtazphdl/notebooks/Dashboard.ipynb", + "input_path": "/tmp/lik815p7/notebooks/Dashboard.ipynb", "output_path": "runs/Dashboard.run.ipynb", "parameters": { - "PAPERMILL_INPUT_PATH": "/tmp/jtazphdl/notebooks/Dashboard.ipynb", + "PAPERMILL_INPUT_PATH": "/tmp/lik815p7/notebooks/Dashboard.ipynb", "PAPERMILL_OUTPUT_PATH": "runs/Dashboard.run.ipynb", - "geodata_path": "/tmp/jtazphdl/data/geodata/geo_data.csv", - "rates_folder": "/tmp/jtazphdl/data/covid-19_rates", - "ts_folder": "/tmp/jtazphdl/data/covid-19_jhu-csse" + "geodata_path": "/tmp/lik815p7/data/geodata/geo_data.csv", + "rates_folder": "/tmp/lik815p7/data/covid-19_rates", + "ts_folder": "/tmp/lik815p7/data/covid-19_jhu-csse" }, - "start_time": "2020-04-07T07:26:26.491817", + "start_time": "2020-04-08T07:28:14.469653", "version": "1.1.0" } }, diff --git a/runs/covidtracking-dashboard.ipynb b/runs/covidtracking-dashboard.ipynb index 3e4d37e02ecafa73536eb1710b66668d133b2d43..ea0e78006cb935347a38ca2aa365cd34946eaf2f 100644 --- a/runs/covidtracking-dashboard.ipynb +++ b/runs/covidtracking-dashboard.ipynb @@ -5,10 +5,10 @@ "execution_count": 1, "metadata": { "papermill": { - "duration": 0.792725, - "end_time": "2020-04-07T07:26:07.289023", + "duration": 0.504913, + "end_time": "2020-04-08T07:28:09.937043", "exception": false, - "start_time": "2020-04-07T07:26:06.496298", + "start_time": "2020-04-08T07:28:09.432130", "status": "completed" }, "tags": [] @@ -27,10 +27,10 @@ "execution_count": 2, "metadata": { "papermill": { - "duration": 0.021587, - "end_time": "2020-04-07T07:26:07.325031", + "duration": 0.025501, + "end_time": "2020-04-08T07:28:09.979872", "exception": false, - "start_time": "2020-04-07T07:26:07.303444", + "start_time": "2020-04-08T07:28:09.954371", "status": "completed" }, "tags": [] @@ -51,10 +51,10 @@ "execution_count": 3, "metadata": { "papermill": { - "duration": 0.019299, - "end_time": "2020-04-07T07:26:07.355022", + "duration": 0.026687, + "end_time": "2020-04-08T07:28:10.019076", "exception": false, - "start_time": "2020-04-07T07:26:07.335723", + "start_time": "2020-04-08T07:28:09.992389", "status": "completed" }, "tags": [ @@ -71,10 +71,10 @@ "execution_count": 4, "metadata": { "papermill": { - "duration": 0.020462, - "end_time": "2020-04-07T07:26:07.387250", + "duration": 0.022895, + "end_time": "2020-04-08T07:28:10.055410", "exception": false, - "start_time": "2020-04-07T07:26:07.366788", + "start_time": "2020-04-08T07:28:10.032515", "status": "completed" }, "tags": [ @@ -84,7 +84,7 @@ "outputs": [], "source": [ "# Parameters\n", - "data_path = \"/tmp/4f2taozu/data/covidtracking\"\n" + "data_path = \"/tmp/k4uq5nii/data/covidtracking\"\n" ] }, { @@ -92,10 +92,10 @@ "execution_count": 5, "metadata": { "papermill": { - "duration": 0.177435, - "end_time": 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"2020-04-07T07:26:05.654270", + "start_time": "2020-04-08T07:28:08.594765", "version": "1.1.0" } }, diff --git a/runs/italy-covid-19.ipynb b/runs/italy-covid-19.ipynb index 512b4c494bec1519dc8a6366fef72a37568819a1..33783e4f34dd0c4decbaa6f6b0bf9c9efc2abd59 100644 --- a/runs/italy-covid-19.ipynb +++ b/runs/italy-covid-19.ipynb @@ -4,10 +4,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.021927, - "end_time": "2020-04-07T07:26:17.851924", + "duration": 0.029104, + "end_time": "2020-04-08T07:27:56.692710", "exception": false, - "start_time": "2020-04-07T07:26:17.829997", + "start_time": "2020-04-08T07:27:56.663606", "status": "completed" }, "tags": [] @@ -23,10 +23,10 @@ "execution_count": 1, "metadata": { "papermill": { - "duration": 0.042551, - "end_time": "2020-04-07T07:26:17.910855", + "duration": 0.091793, + "end_time": "2020-04-08T07:27:56.797917", "exception": false, - "start_time": "2020-04-07T07:26:17.868304", + "start_time": "2020-04-08T07:27:56.706124", "status": "completed" }, "tags": [] @@ -42,10 +42,10 @@ "execution_count": 2, "metadata": { "papermill": { - "duration": 0.614232, - "end_time": "2020-04-07T07:26:18.540574", + "duration": 1.271051, + "end_time": "2020-04-08T07:27:58.090910", "exception": false, - "start_time": "2020-04-07T07:26:17.926342", + "start_time": "2020-04-08T07:27:56.819859", "status": "completed" }, "tags": [] @@ -68,10 +68,10 @@ "execution_count": 3, "metadata": { "papermill": { - "duration": 0.04295, - "end_time": "2020-04-07T07:26:18.602300", + "duration": 0.051506, + "end_time": "2020-04-08T07:27:58.165832", "exception": false, - "start_time": "2020-04-07T07:26:18.559350", + "start_time": "2020-04-08T07:27:58.114326", "status": "completed" }, "tags": [] @@ -92,10 +92,10 @@ "execution_count": 4, "metadata": { "papermill": { - "duration": 0.039252, - "end_time": "2020-04-07T07:26:18.658367", + "duration": 0.053451, + "end_time": "2020-04-08T07:27:58.238883", "exception": false, - "start_time": "2020-04-07T07:26:18.619115", + "start_time": "2020-04-08T07:27:58.185432", "status": "completed" }, "tags": [ @@ -112,10 +112,10 @@ "execution_count": 5, "metadata": { "papermill": { - "duration": 0.037651, - "end_time": "2020-04-07T07:26:18.712229", + "duration": 0.051747, + "end_time": "2020-04-08T07:27:58.314054", "exception": false, - "start_time": "2020-04-07T07:26:18.674578", + "start_time": "2020-04-08T07:27:58.262307", "status": "completed" }, "tags": [ @@ -125,7 +125,7 @@ "outputs": [], "source": [ "# Parameters\n", - "data_folder = \"/tmp/7sfzizjj/data/covid-19-italy\"\n" + "data_folder = \"/tmp/_coxk2vv/data/covid-19-italy\"\n" ] }, { @@ -133,10 +133,10 @@ "execution_count": 6, "metadata": { "papermill": { - "duration": 0.049869, - "end_time": "2020-04-07T07:26:18.777306", + "duration": 0.097105, + "end_time": "2020-04-08T07:27:58.433663", "exception": false, - "start_time": "2020-04-07T07:26:18.727437", + "start_time": "2020-04-08T07:27:58.336558", "status": "completed" }, "tags": [] @@ -156,10 +156,10 @@ "execution_count": 7, "metadata": { "papermill": { - "duration": 0.045029, - "end_time": "2020-04-07T07:26:18.837924", + "duration": 0.059387, + "end_time": "2020-04-08T07:27:58.516353", "exception": false, - "start_time": "2020-04-07T07:26:18.792895", + "start_time": "2020-04-08T07:27:58.456966", "status": "completed" }, "tags": [] @@ -175,10 +175,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.012953, - "end_time": "2020-04-07T07:26:18.868071", + "duration": 0.014635, + "end_time": "2020-04-08T07:27:58.555940", "exception": false, - "start_time": "2020-04-07T07:26:18.855118", + "start_time": "2020-04-08T07:27:58.541305", "status": "completed" }, "tags": [] @@ -192,10 +192,10 @@ "execution_count": 8, "metadata": { "papermill": { - "duration": 0.100409, - "end_time": "2020-04-07T07:26:18.981728", + "duration": 0.150261, + "end_time": "2020-04-08T07:27:58.717472", "exception": false, - "start_time": 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