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Commit 8a3562df authored by CI-bot's avatar CI-bot Committed by renku 0.10.4
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renku rerun data/covidtracking/states-metadata.json data/covidtracking/states-daily.json

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1 merge request!359Automatic update - auto-update_2020-11-04_08-01
Pipeline #100449 failed
Stage: build
    Stage: datasets-update
      Stage: notebooks-update
        Stage: finalize-update
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          .renku/workflow/975bb67340ec472c964083369b804c54.cwl 0 → 100644
          + 120
          − 0
          View file @ 8a3562df
          class: Workflow
          cwlVersion: v1.0
          hints: []
          inputs:
          input_1:
          default: states-metadata.json
          streamable: false
          type: string
          input_2:
          default: states-daily.json
          streamable: false
          type: string
          input_3:
          default: out_folder
          streamable: false
          type: string
          input_4:
          default: data/covidtracking
          streamable: false
          type: string
          input_5:
          default:
          class: File
          path: ../../notebooks/process/download-covidtracking-data.ipynb
          streamable: false
          type: File
          input_6:
          default: runs/download-covidtracking-data.runs.ipynb
          streamable: false
          type: string
          outputs:
          output_2:
          outputSource: step_3/output_0
          streamable: false
          type: File
          output_3:
          outputSource: step_3/output_1
          streamable: false
          type: Directory
          requirements: []
          steps:
          step_1:
          in:
          filename: input_1
          input_directory: step_3/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
          class: InlineJavascriptRequirement
          - &id002
          class: InitialWorkDirRequirement
          listing: $(inputs.input_directory.listing)
          successCodes: []
          temporaryFailCodes: []
          step_2:
          in:
          filename: input_2
          input_directory: step_3/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
          - *id002
          successCodes: []
          temporaryFailCodes: []
          step_3:
          in:
          input_1: input_3
          input_2: input_4
          input_3: input_5
          input_4: input_6
          out:
          - output_1
          - output_0
          run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
          data/covidtracking/states-daily.json LFS
          + 2
          − 2
          View file @ 8a3562df
          source diff could not be displayed: it is stored in LFS. Options to address this: view the blob.
          data/covidtracking/states-metadata.json LFS
          + 2
          − 2
          View file @ 8a3562df
          source diff could not be displayed: it is stored in LFS. Options to address this: view the blob.
          runs/download-covidtracking-data.runs.ipynb
          + 67
          − 67
          View file @ 8a3562df
          %% Cell type:code id: tags:
          ``` python
          import requests
          import os
          import pandas as pd
          ```
          %% Cell type:code id: tags:parameters
          ``` python
          out_folder = "../data/covidtracking/"
          PAPERMILL_OUTPUT_PATH = None
          ```
          %% Cell type:code id: tags:injected-parameters
          ``` python
          # Parameters
          PAPERMILL_INPUT_PATH = "/tmp/qj7q4luy/notebooks/process/download-covidtracking-data.ipynb"
          PAPERMILL_INPUT_PATH = "/tmp/po7g_8x1/notebooks/process/download-covidtracking-data.ipynb"
          PAPERMILL_OUTPUT_PATH = "runs/download-covidtracking-data.runs.ipynb"
          out_folder = "data/covidtracking"
          ```
          %% Cell type:markdown id: tags:
          # Download state metadata
          Download a dataset of URLs for data for each US state and several territories. See [Google Doc](https://docs.google.com/spreadsheets/d/18oVRrHj3c183mHmq3m89_163yuYltLNlOmPerQ18E8w/htmlview?sle=true).
          %% Cell type:code id: tags:
          ``` python
          url = 'http://covidtracking.com/api/states/info'
          r = requests.get(url, allow_redirects=True)
          states_metadata_json = r.content
          ```
          %% Cell type:code id: tags:
          ``` python
          # save the result
          if PAPERMILL_OUTPUT_PATH:
          out_path = os.path.join(out_folder, 'states-metadata.json')
          with open(out_path, 'wb') as f:
          f.write(states_metadata_json)
          ```
          %% Cell type:code id: tags:
          ``` python
          metadata_df = pd.read_json(states_metadata_json)
          print(len(metadata_df), "states and territories have metadata")
          metadata_df.head(2)
          ```
          %% Output
          56 states and territories have metadata
          state notes \
          0 AK Alaska combines PCR and antigen tests in the t...
          1 AL Alabama combines PCR and antigen tests in the ...
          covid19Site \
          0 http://dhss.alaska.gov/dph/Epi/id/Pages/COVID-...
          1 https://alpublichealth.maps.arcgis.com/apps/op...
          covid19SiteSecondary \
          0 https://experience.arcgis.com/experience/ed1c8...
          1 https://alpublichealth.maps.arcgis.com/apps/op...
          covid19SiteTertiary covid19SiteQuaternary \
          0 https://alaska-dhss.maps.arcgis.com/apps/opsda... None
          1 https://services7.arcgis.com/4RQmZZ0yaZkGR1zy/... None
          covid19SiteQuinary twitter \
          0 None @Alaska_DHSS
          1 None @alpublichealth
          covid19SiteOld \
          0 http://dhss.alaska.gov/dph/Epi/id/Pages/COVID-...
          1 http://www.alabamapublichealth.gov/infectiousd...
          covidTrackingProjectPreferredTotalTestUnits \
          0 Specimens
          1 Unclear units
          covidTrackingProjectPreferredTotalTestField totalTestResultsField pui \
          0 totalTestsViral Total Tests (PCR) All data
          1 totalTestsViral Total Tests (PCR) No data
          pum name fips
          0 False Alaska 2
          1 False Alabama 1
          %% Cell type:markdown id: tags:
          # Download daily state data
          %% Cell type:code id: tags:
          ``` python
          url = 'https://covidtracking.com/api/states/daily'
          r = requests.get(url, allow_redirects=True)
          states_daily_json = r.content
          ```
          %% Cell type:code id: tags:
          ``` python
          # save the result
          if PAPERMILL_OUTPUT_PATH:
          out_path = os.path.join(out_folder, 'states-daily.json')
          with open(out_path, 'wb') as f:
          f.write(states_daily_json)
          ```
          %% Cell type:code id: tags:
          ``` python
          data_df = pd.read_json(states_daily_json)
          print(len(data_df), "data points")
          data_df.head(2)
          ```
          %% Output
          13663 data points
          13775 data points
          date state positive probableCases negative pending \
          0 20201101 AK 16705.0 NaN 587852.0 NaN
          1 20201101 AL 193985.0 28746.0 1187341.0 NaN
          0 20201103 AK 17448.0 NaN 607307.0 NaN
          1 20201103 AL 195929.0 29302.0 1196422.0 NaN
          totalTestResultsSource totalTestResults hospitalizedCurrently \
          0 totalTestsViral 604207.0 98.0
          1 totalTestsViral 1352580.0 967.0
          0 totalTestsViral 624755.0 97.0
          1 totalTestsViral 1363049.0 1022.0
          hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \
          0 NaN ... 604557 1 0
          1 20450.0 ... 1381326 6 0
          0 NaN ... 624755 0 0
          1 20901.0 ... 1392351 14 451
          hash commercialScore \
          0 0fe81cb4b3a17588cfde8bbd309c3f0f2e786fd2 0
          1 0bd0f2572848cf6f46a651c076d32afceb8dc6a1 0
          0 e4b7b20d6a7724e14ce53e37e1d543c6bf1176c9 0
          1 f6dd94c1b534c3e4a74e78d1859fcc12ae1ef103 0
          negativeRegularScore negativeScore positiveScore score grade
          0 0 0 0 0
          1 0 0 0 0
          [2 rows x 55 columns]
          ......
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