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HakaiInstitute / GEM-in-a-box-dataset-repository-template

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Suggested daily workflow #7

Open timvdstap opened 2 months ago

timvdstap commented 2 months ago

Below a suggested daily workflow, as modified from: https://github.com/HakaiInstitute/GEM-in-a-box-dataset-repository-template/issues/3

Before Field Sampling

  1. Download the [survey sheet] and [instrument data sheet template] to your local device, and print them.

Field Steps

  1. On a survey, a user should fill a paper copy of the survey data sheet.
  2. Go to a sampling site, and let the instruments and the Niskin bottle soak at the target depth for at least 5 minutes.
  3. Send niskin bottle messenger down and save that as Instrument Sample Time.
  4. Populate the rest of the survey and instrument data sheets accordingly.
  5. Confirm all data is collected before moving on to the next site.

Post-Field Steps - Survey

  1. Take a picture of the survey template sheet filled out in the field, saving it locally as {YYYY-MM-DD}_survey_raw.jpeg.
  2. Download the [survey template data sheet].
  3. Transcribe the survey sheet into the survey template data sheet, saving it locally as {YYYY-MM-DD}_survey_final.csv
  4. Update the stations.csv file as needed and upload to the root of the GitHub repository.

Post-Field Steps - Instruments

  1. Download the data from the PME miniDOT and CTD-diver, save them on your local device in the original format.
  2. Rename the raw data files from the instrument following the naming convention: {YYYY-MM-DD}_Instruments_raw
  3. Download the [Instrument data template] and populate it.
  4. Save the Instrument data template locally, renaming it following the naming convention: {YYYY-MM-DD}_Instruments_processed
  5. Conduct QAQC, recording any modifications, removals or additions to the data in a Changelog.txt file.
  6. Save, locally, the final processed file as {YYYY-MM-DD}_Instruments_final.csv

Lab Analysis Steps

  1. Download the [Aquafluor data sheet template] and [DR1900 data sheet template] to your local device and print them.
  2. Analyze the water samples following the protocol(s), recording the data on data sheets.
  3. Take a picture of the physical Aquafluor and DR1900 data sheets, saving it locally as e.g., {YYYY-MM-DD}_Aquafluor_raw_datasheet1.jpeg
  4. Transcribe the data from the physical data sheet to the Aquafluor and DR1900 data sheets, performing an initial round of QAQC, and save them locally as e.g., {YYYY-MM-DD}_Aquafluor_processed
  5. Conduct QAQC, recording any modifications, removals or additions to the data in a Changelog.txt file.
  6. Save, locally, the final processed file as e.g., {YYYY-MM-DD}_Aquafluor_final.csv.

Data Processing

  1. Create a new survey-specific folder within the /data folder, following the naming convention {YYYY-MM-DD_survey}. See here for a detailed step-by-step way to create new folder, with their relevant subfolders (Aquafluor, DR1900, Instruments). When committing these changes, make sure to select create a new branch for this commit and start a pull request**.
  2. Make sure to navigate to the appropriate branch.
  3. Upload the _raw and _processed survey sheets into the root of the survey-specific folder.
  4. Upload the _raw, _processed and _final data files from the instrument and lab analyses, along with the changelog files, to the appropriate folders.
  5. Troubleshoot any issues that may have arisen when attempting to merge the branch into main.