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Ocn 027 rw0 #292

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clairehemmerly
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@clairehemmerly clairehemmerly commented Jun 7, 2022 •
edited by chrowe
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Checklist for Reviewing a Pre-Processing Script

  • Does the python script contain the following 4 sections: Download data and save to your data directory, Process data, Upload processed data to Carto/Upload processed data to Google Earth Engine, Upload original data and processed data to Amazon S3 storage?
  • Does the script have the standardized variable names for: dataset_name, raw_data_file, processed_data_file?
  • Does the script create and use a 'data' directory?
  • Does the script use a python module to automatically download the data? If this is not possible, are there explicit instructions for how to download the data (step by step with instructions about every input parameter and button to click to find the exact data) and does it use shutil to move the data from 'Downloads' into the data directory?
  • Is the script automated as much as possible to minimize rewriting code the next time the dataset updates (ex 1: can you automatically pull out column names instead of typing them yourself? ex 2: if you are dropping columns with no data, did you use pandas to find the nodata columns instead of dropping the column by name?)
  • Are there comments on almost every line of code to explicitly state what is being done and why?
  • Are you uploading to the correct AWS location?
  • For GEE scripts, did you explicitly define the band manifest with a pyramiding policy so that we can easily change it later if we need to?
  • Does the README contain all relevant links?
  • Does the README state the original file type?
  • Does the README list all of the processing steps that were taken in the script?
  • For netcdfs, does the README state which variables were pulled from the netcdf?
  • Did you use the util functions whenever possible?
  • Have you checked the processed data file on your computer to make sure it matches the data you uploaded to Carto? (spaces or symbol names in column titles often get changed in the upload process-please change these before uploading so that the backed up processed data matches the data on Carto)
  • Does the folder name and python script file name match the dataset_name variable in the script? Are they all lowercase? Does the processing script end in '_processing.py'? (this part is often forgotten)

@clairehemmerly clairehemmerly requested a review from chrowe June 7, 2022 16:42
@clairehemmerly clairehemmerly self-assigned this Jun 7, 2022
chrowe
chrowe requested changes Jul 8, 2022
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A few minor change requests and a couple questions but overall looks good.
Only thing I didn't check was if the column names in Carto match those in the files sent to s3. Did you do that?

ocn_027a_rw0_nitrogen_plumes/README.md Outdated

You can also download the original dataset [directly through Resource Watch](http://wri-public-data.s3.amazonaws.com/resourcewatch/raster/ocn_027_rw0_nitrogen_plumes.zip), or [from the source website](https://knb.ecoinformatics.org/view/urn%3Auuid%3Ac7bdc77e-6c7d-46b6-8bfc-a66491119d07).

###### Note: This dataset processing was done by Claire Hemmerly, and QC'd by [Chris Rowe](https://www.wri.org/profile/chris-rowe).
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You can add any link here if you want.

ocn_027a_rw0_nitrogen_plumes/README.md Outdated Show resolved Hide resolved
ocn_027a_rw0_nitrogen_plumes/README.md Outdated

You can view the processed Wastewater Plumes in Coastal Areas dataset [on Resource Watch](https://resourcewatch.org/data/explore/11804f04-d9c7-47b9-8d27-27ce6ed6c042).

You can also download the original dataset [directly through Resource Watch](http://wri-public-data.s3.amazonaws.com/resourcewatch/raster/ocn_027_rw0_nitrogen_plumes.zip), or [from the source website](https://knb.ecoinformatics.org/view/urn%3Auuid%3Ac7bdc77e-6c7d-46b6-8bfc-a66491119d07).
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Since this if a raster file we don't link to our s3 version. You can just link to the source.
Side note, do you know why the zip file on our s3 is so large? My browser says it is 11GB but the source file looks to be 250MB.

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@clairehemmerly clairehemmerly Jul 12, 2022 •
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I compressed the zipfile and uploaded to the correct folder. I deleted the one that was 11G

ocn_027a_rw0_nitrogen_plumes/README.md Outdated Show resolved Hide resolved
ocn_027b_rw0_wastewater_pourpoints/ocn_027b_rw0_wastewater_pourpoints_processing.py

# convert the data type of columns to integer
for col in gdf.columns[1:9]:
gdf[col] = gdf[col].fillna(0).astype('int')
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Are you sure we want na values to be zero? Are there any existing zero values?

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@clairehemmerly clairehemmerly Jul 13, 2022 •
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Only NA values are in the columns that show % nitrogen input, which we're not using, and the same rows have 0 for the nitrogen input in g/yr, so I think updating the NAs to 0 should be fine. I had trouble creating the processed shapefile when the values were floats not integers, I got an error basically saying the numbers were too big.

ocn_027c_rw0_wastewater_watersheds/README.md Outdated Show resolved Hide resolved
ocn_027c_rw0_wastewater_watersheds/README.md Outdated Show resolved Hide resolved
ocn_027c_rw0_wastewater_watersheds/ocn_027c_rw0_wastewater_watersheds_processing.py

# convert the data type of columns to integer
for col in gdf.columns[1:9]:
gdf[col] = gdf[col].fillna(0).astype('int')
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Again, just want to make sure we are accurately translating the data here.

ocn_027b_rw0_wastewater_pourpoints/ocn_027b_rw0_wastewater_pourpoints_processing.py Outdated
'''

# load in the polygon shapefile
shapes = os.path.join(raw_data_file_unzipped, 'effluent_N_pourpoints_all.shp')
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Can you use processed_data_file here instead of shapes for consistency with our other scripts?

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Actually I think the main thing is that the final thing you upload is called processed_data_file.

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Ive updated this section, let me know if it looks ok

ocn_027c_rw0_wastewater_watersheds/ocn_027c_rw0_wastewater_watersheds_processing.py
set_default_credentials(username=CARTO_USER, base_url="https://{user}.carto.com/".format(user=CARTO_USER),api_key=CARTO_KEY)

# upload data frame to Carto
to_carto(gdf, dataset_name + '_edit', if_exists='replace')
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For consistency can you use processed_data_file instead of gdf?

chrowe
chrowe reviewed Jul 12, 2022
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ocn_027a_rw0_nitrogen_plumes/ocn_027a_rw0_nitrogen_plumes_processing.py Outdated
Upload original data and processed data to Amazon S3 storage
'''
# initialize AWS variables
aws_bucket = 'wri-public-data'
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This should actually be aws_bucket = 'wri-projects' for raster datasets.

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fixed

@clairehemmerly
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I added the processed data file steps and checked the col names, should match now

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