Script to add species and region information to watershed map

[corviday]

This command line script should take two inputs - a shapefile (map file) containing a number of named regions, and a CSV file (spreadsheet) that, for each watershed, lists whether a particular group of salmon (conservation unit) is present in that region. We'd like the information about which species of salmon is present to be added to the map file so it can be displayed on the BC-SRIF portal.

CSV FORMAT The CSV has a row for each watershed, identified by watershed code (WTRSHDGRPC), and a column for each individual salmon population; it looks like this:

WTRSHDGRPC	cc_ck_509	cc_ck_510
PORI	0	1
UPET	0	0
LCHL	0	0
GUIC	0	0

This tells us that the salmon population cc_ck_509 is not present in the PORI watershed, but cc_ck_510 is present in this watershed. The first part of the salmon population code is the region:

Abbreviation	Region
cc	Central Coast
fr	Fraser
hg	Haida Gwaii
na	Nass
sk	Skeet
vimi	Vancouver Island and Mainland Inlets

The second part of the salmon population code is the species:

Abbreviation	Species
ck	Chinook
cm	Chum
co	Coho
pke	Pink Even
pko	Pink Odd
sel	Sockeye Lake
ser	Sockeye River

For each watershed, we'd like to be able to display on the website which region it was in and which salmon species are present. In the shapefile, we'd like to add a region property and an attribute for each of the species of salmon, which we can figure out from the codes of the salmon populations present in each watershed. So add properties named "region", "chinook", "chum", etc. I think spaces might cause trouble in property names, so use an underscore for the two-word species names.

So if, for example, the salmon group cc_ck_509 is present in watershed PORI, this is a population of Chinook salmon on the Central Coast, and we know that PORI is in the Central Coast region and is home to some Chinook salmon. cc_pke_304 might also be marked as present in PORI, which would mean Pink Even salmon were present in this watershed as well.

Set the region property to the name of the region (all salmon populations in a watershed should have the same regio, a watershed can only be in one region) and set the species property to 1 if one or more of the salmon populations present are that species, and 0 otherwise.

Useful notes:

• a shapefile can be viewed with the free but inelegant program called QGIS - if you open the file and click on one of the regions, you can see its attributes, a useful way to tell if the script is working correctly
• The CSV file can be viewed either with a text editor, or with any spreadsheet viewing program
• the CSV file is hand-made by a biologist and might contain misspelled region names or missing values or something, the script should check for these and display a helpful error message if it finds one
• python has a pretty nice csv-reading library
• python has a shapefile-reading library but I've never used it and don't know how good it is
• python has the argparse library, which is a really nice way to handle processing inputs to command line scripts
• In this repository, which is a library of data-processsing scripts saved so that they can be reused or checked later, new data-processing scripts are each added inside a new folder in the actions directory, and each data-processing script should have a DESCRIPTION explaining what the script does with examples on how to use it
• formal pytesting isn't necessary for data-processing scripts, but definitely make sure the data you're outputting looks correct, hand check a few different regions in QGIS, the reviewer will do this too

[corviday]

We have changed how we handle salmon populations; they are now stored in a postGIS database, instead of shapefiles. This script is no longer needed (though we need a script to add population data to the postGIS database instead).