diff --git a/.renku/workflow/14104787d8d6409eb91c0bf4a5a2022e.cwl b/.renku/workflow/14104787d8d6409eb91c0bf4a5a2022e.cwl new file mode 100644 index 0000000000000000000000000000000000000000..29ae3f38d615c6a14ddc344b9a14afa97ff61c50 --- /dev/null +++ b/.renku/workflow/14104787d8d6409eb91c0bf4a5a2022e.cwl @@ -0,0 +1,120 @@ +class: Workflow +cwlVersion: v1.0 +hints: [] +inputs: + input_1: + default: out_folder + streamable: false + type: string + input_2: + default: data/covidtracking + streamable: false + type: string + input_3: + default: + class: File + path: ../../notebooks/process/download-covidtracking-data.ipynb + streamable: false + type: File + input_4: + default: runs/download-covidtracking-data.runs.ipynb + streamable: false + type: string + input_5: + default: states-daily.json + streamable: false + type: string + input_6: + default: states-metadata.json + streamable: false + type: string +outputs: + output_1: + outputSource: step_1/output_0 + streamable: false + type: File + output_3: + outputSource: step_1/output_1 + streamable: false + type: Directory +requirements: [] +steps: + step_1: + in: + input_1: input_1 + input_2: input_2 + input_3: input_3 + input_4: input_4 + out: + - output_0 + - output_1 + run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl + step_2: + in: + filename: input_5 + input_directory: step_1/output_1 + out: + - output_file + run: + arguments: [] + baseCommand: + - 'true' + class: CommandLineTool + cwlVersion: v1.0 + hints: [] + inputs: + filename: + default: states-daily.json + streamable: false + type: string + input_directory: + streamable: false + type: Directory + outputs: + output_file: + outputBinding: + glob: $(inputs.filename) + streamable: false + type: File + permanentFailCodes: [] + requirements: + - &id001 + class: InlineJavascriptRequirement + - &id002 + class: InitialWorkDirRequirement + listing: $(inputs.input_directory.listing) + successCodes: [] + temporaryFailCodes: [] + step_3: + in: + filename: input_6 + input_directory: step_1/output_1 + out: + - output_file + run: + arguments: [] + baseCommand: + - 'true' + class: CommandLineTool + cwlVersion: v1.0 + hints: [] + inputs: + filename: + default: states-metadata.json + streamable: false + type: string + input_directory: + streamable: false + type: Directory + outputs: + output_file: + outputBinding: + glob: $(inputs.filename) + streamable: false + type: File + permanentFailCodes: [] + requirements: + - *id001 + - *id002 + successCodes: [] + temporaryFailCodes: [] diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json index 8cd963bef55d876806a1a6e42587abe5e955e9d8..fc773df257431168a97018ddb04a386d39783438 100644 --- a/data/covidtracking/states-daily.json +++ b/data/covidtracking/states-daily.json @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:3a2d54ba98b1707b5ab739f7a08d04feaa9ef0261ba8637fd953675d4b52103c -size 15133509 +oid sha256:ffad157a714e91e50e3420067f6bc43529fdcb19735766903153628ec7bab103 +size 15208829 diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json index 39f1b7dabbfd29b62fa5e0ab55cc9bc106f23884..b3cfc9ac4148e79aee78654c0e2d853e249580be 100644 --- a/data/covidtracking/states-metadata.json +++ b/data/covidtracking/states-metadata.json @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:132b77335850da7e0708e078078c476d7595248af97bba2edf4e495a335e2c6e -size 81151 +oid sha256:74b334c56573d929a59f7cb8efa7d2e218a05d81060ac6d287f0704d0db9f40b +size 81413 diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb index 5ebb6f1000de0db941ebbc9924152325180f455e..18fe29ee3f29acccb3bec4153682e0d1e0f2aa02 100644 --- a/runs/download-covidtracking-data.runs.ipynb +++ b/runs/download-covidtracking-data.runs.ipynb @@ -5,10 +5,10 @@ "execution_count": 1, "metadata": { "papermill": { - "duration": 4.181312, - "end_time": "2020-09-23T07:35:21.010050", + "duration": 3.711103, + "end_time": "2020-09-24T07:35:55.897522", "exception": false, - "start_time": "2020-09-23T07:35:16.828738", + "start_time": "2020-09-24T07:35:52.186419", "status": "completed" }, "tags": [] @@ -25,10 +25,10 @@ "execution_count": 2, "metadata": { "papermill": { - "duration": 0.01892, - "end_time": "2020-09-23T07:35:21.042851", + "duration": 0.027146, + "end_time": "2020-09-24T07:35:55.939885", "exception": false, - "start_time": "2020-09-23T07:35:21.023931", + "start_time": "2020-09-24T07:35:55.912739", "status": "completed" }, "tags": [ @@ -46,10 +46,10 @@ "execution_count": 3, "metadata": { "papermill": { - "duration": 0.019395, - "end_time": "2020-09-23T07:35:21.074425", + "duration": 0.031292, + "end_time": "2020-09-24T07:35:55.985668", "exception": false, - "start_time": "2020-09-23T07:35:21.055030", + "start_time": "2020-09-24T07:35:55.954376", "status": "completed" }, "tags": [ @@ -59,7 +59,7 @@ "outputs": [], "source": [ "# Parameters\n", - "PAPERMILL_INPUT_PATH = \"/tmp/o8q1c8tx/notebooks/process/download-covidtracking-data.ipynb\"\n", + "PAPERMILL_INPUT_PATH = \"/tmp/hhqn2uzg/notebooks/process/download-covidtracking-data.ipynb\"\n", "PAPERMILL_OUTPUT_PATH = \"runs/download-covidtracking-data.runs.ipynb\"\n", "out_folder = \"data/covidtracking\"\n" ] @@ -68,10 +68,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.007765, - "end_time": "2020-09-23T07:35:21.089543", + "duration": 0.008503, + "end_time": "2020-09-24T07:35:56.008313", "exception": false, - "start_time": "2020-09-23T07:35:21.081778", + "start_time": "2020-09-24T07:35:55.999810", "status": "completed" }, "tags": [] @@ -87,10 +87,10 @@ "execution_count": 4, "metadata": { "papermill": { - "duration": 0.628909, - "end_time": "2020-09-23T07:35:21.725778", + "duration": 0.325836, + "end_time": "2020-09-24T07:35:56.341140", "exception": false, - "start_time": "2020-09-23T07:35:21.096869", + "start_time": "2020-09-24T07:35:56.015304", "status": "completed" }, "tags": [] @@ -107,10 +107,10 @@ "execution_count": 5, "metadata": { "papermill": { - "duration": 0.018332, - "end_time": "2020-09-23T07:35:21.755795", + "duration": 0.028059, + "end_time": "2020-09-24T07:35:56.382919", "exception": false, - "start_time": "2020-09-23T07:35:21.737463", + "start_time": "2020-09-24T07:35:56.354860", "status": "completed" }, "tags": [] @@ -129,10 +129,10 @@ "execution_count": 6, "metadata": { "papermill": { - "duration": 0.073565, - "end_time": "2020-09-23T07:35:21.836599", + "duration": 0.079429, + "end_time": "2020-09-24T07:35:56.475405", "exception": false, - "start_time": "2020-09-23T07:35:21.763034", + "start_time": "2020-09-24T07:35:56.395976", "status": "completed" }, "tags": [] @@ -270,10 +270,10 @@ "cell_type": "markdown", "metadata": { "papermill": { - "duration": 0.007067, - "end_time": "2020-09-23T07:35:21.854979", + "duration": 0.007668, + "end_time": "2020-09-24T07:35:56.497150", "exception": false, - "start_time": "2020-09-23T07:35:21.847912", + "start_time": "2020-09-24T07:35:56.489482", "status": "completed" }, "tags": [] @@ -287,10 +287,10 @@ "execution_count": 7, "metadata": { "papermill": { - "duration": 25.11081, - "end_time": "2020-09-23T07:35:46.972922", + "duration": 25.363958, + "end_time": "2020-09-24T07:36:21.868028", "exception": false, - "start_time": "2020-09-23T07:35:21.862112", + "start_time": "2020-09-24T07:35:56.504070", "status": "completed" }, "tags": [] @@ -307,10 +307,10 @@ "execution_count": 8, "metadata": { "papermill": { - "duration": 0.034722, - "end_time": "2020-09-23T07:35:47.021928", + "duration": 0.061035, + "end_time": "2020-09-24T07:36:21.948005", "exception": false, - "start_time": "2020-09-23T07:35:46.987206", + "start_time": "2020-09-24T07:36:21.886970", "status": "completed" }, "tags": [] @@ -329,10 +329,10 @@ "execution_count": 9, "metadata": { "papermill": { - "duration": 0.562298, - "end_time": "2020-09-23T07:35:47.592568", + "duration": 0.553683, + "end_time": "2020-09-24T07:36:22.518379", "exception": false, - "start_time": "2020-09-23T07:35:47.030270", + "start_time": "2020-09-24T07:36:21.964696", "status": "completed" }, "tags": [] @@ -342,7 +342,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "11354 data points\n" + "11410 data points\n" ] }, { @@ -392,21 +392,21 @@ "
\n", "