Add function to Optionally get site.info if not present
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| Original file line number | Diff line number | Diff line change |
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| ##' Get new site info using provided site information | ||
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| ##' | ||
| ##' @title Get New Site Info | ||
| ##' @param site a dataframe with site information including id, lat, lon, and time_zone. | ||
| ##' @param con Database connection object. | ||
| ##' @return a dataframe with new site information on lat, lon and time_zone | ||
| ##' @export | ||
| ##' @author Abhinav Pandey | ||
| ##' @importFrom digest digest | ||
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Member
There was a problem hiding this comment. What does this do? First, as far as I can tell this function is never used here. Second, where it is used I don't see why it can't be called by namespace |
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| ##' | ||
| ##' @examples | ||
| ##' get.new.site(site=data.frame(id=1,lat=40.1,lon=-88.2, time_zone = "UTC"), con = NULL) | ||
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| get.new.site <- function(site, con = NULL) { | ||
| if (is.null(con)) { | ||
| PEcAn.logger::logger.debug("DB connection is closed. Trying to generate a new site ID or use pre-existing one.") | ||
| # No DB connection present. Generate a new ID using one of below steps: | ||
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| if (is.null(site$id) | is.na(site$id)) { | ||
| if ((!is.null(site$lat) && !is.null(site$lon)) && | ||
| (!is.na(site$lat) && !is.na(site$lon)) | ||
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| ) { | ||
| site.id <- paste0(site$lat, "_", site$lon) | ||
| new.site <- data.frame( | ||
| id = as.numeric(site.id), | ||
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Member
There was a problem hiding this comment. the as.numeric here seems like it's going to always return NA given how site.id is constructed |
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| lat = site$lat, | ||
| lon = site$lon | ||
| ) | ||
| str_ns <- paste0(new.site$lat, "_", new.site$lon) | ||
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Member
There was a problem hiding this comment. this seems redundant with site.id |
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| } # lat/lon present but ID is absent | ||
| # Use Pre-existing normalised lat/lon | ||
| else { | ||
| PEcAn.logger::logger.warn("Site dataframe does not have an id column") | ||
| site.id <- generate_site_id() | ||
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Member
There was a problem hiding this comment. This function has two non-optional arguments that aren't being specified, so how is this code not throwing an error when you run it? |
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| PEcAn.logger::logger.info(paste0("Generated siteID:", site.id)) | ||
| # Optionally, create a new site data frame with the random ID | ||
| new.site <- data.frame( | ||
| id = site.id, | ||
| lat = NULL, | ||
| lon = NULL | ||
| ) | ||
| str_ns <- paste0(new.site$id %/% 1e+09, "_", new.site$id %% 1e+09) | ||
| # We used a different str_ns as identifier here due to absence of lat/lon | ||
| } | ||
| # ID as well as lat/lon absent. | ||
| # Return a WARN as we will be unable to identify such an instance due to lack of information. | ||
| # We'll try to Generate a new ID similar to previous ones. | ||
| } else { | ||
| if ((!is.null(site$lat) && !is.null(site$lon)) && | ||
| (!is.na(site$lat) && !is.na(site$lon)) | ||
| ) { | ||
| new.site <- data.frame( | ||
| id = as.numeric(site$id), | ||
| lat = site$lat, | ||
| lon = site$lon | ||
| ) | ||
| str_ns <- paste0(new.site$lat, "-", new.site$lon) | ||
| } # siteId as well as lat/lon present | ||
| else { | ||
| new.site <- data.frame( | ||
| id = site$id, | ||
| lat = NULL, | ||
| lon = NULL | ||
| ) | ||
| str_ns <- paste0(new.site$id %/% 1e+09, "-", new.site$id %% 1e+09) | ||
| } # siteId present but lat/lon absent | ||
| } | ||
| } else { | ||
| # Check if site dataframe has an id column | ||
| if (is.null(site$id) | is.na(site$id)) { | ||
| PEcAn.logger::logger.warn("Site dataframe does not have an id column. Generating a unique ID") | ||
| if ((!is.null(site$lat) && !is.null(site$lon)) && | ||
| (!is.na(site$lat) && !is.na(site$lon)) | ||
| ) { | ||
| PEcAn.logger::logger.info(paste0("Generated siteID using lat and lon:", site.id)) | ||
| site.id <- generate_site_id(site$lat, site$lon) | ||
| new.site <- data.frame( | ||
| id = as.numeric(site.id), | ||
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Member
There was a problem hiding this comment. does this id need to be numeric? If so, why? Is the algorithm generating it guaranteed to produce numbers?
Member
There was a problem hiding this comment. It won't be numeric if using digest as is. |
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| lat = site$lat, | ||
| lon = site$lon | ||
| ) | ||
| str_ns <- paste0(site$lat, "-", site$lon) | ||
| } else { | ||
| PEcAn.logger::logger.severe("Missing site-id, site lat & site-lon. Stopping the process due to lack of information") | ||
| } | ||
| } else { | ||
| # setup site database number, lat, lon and name and copy for format.vars if new input | ||
| if ((!is.null(site$lat) && !is.null(site$lon)) | | ||
| (!is.na(site$lat) && !is.na(site$lon)) | ||
| ) { | ||
| new.site <- data.frame( | ||
| id = as.numeric(site$id), | ||
| lat = site$lat, | ||
| lon = site$lon | ||
| ) | ||
| str_ns <- paste0(site$lat, "_", site$lon) | ||
| } | ||
| } | ||
| } | ||
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| site.info <- list(new.site = new.site, str_ns = str_ns) | ||
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Member
There was a problem hiding this comment. Q in live review: why this structure? A: to match what's expected at met.process line 165
Contributor
Author
There was a problem hiding this comment. Detailed Explanation : Current structure is followed to match data flow of what information is later on utilised in |
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| return(site.info) | ||
| } | ||
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| #' Generate a unique site ID from latitude/longitude | ||
| #' | ||
| #' @param lat Latitude value | ||
| #' @param lon Longitude value | ||
| #' @return A unique string ID generated by hashing the lat/lon values | ||
| #' @details This function is intended for database-less runs only by generating | ||
| #' a unique site ID by hashing the rounded lat/lon coordinates. | ||
| #' | ||
| #' @author Abhinav Pandey | ||
| #' @export | ||
| generate_site_id <- function(lat, lon) { | ||
| latlon_str <- paste0(lat, lon) | ||
| uid <- digest::digest(latlon_str, algo = "xxhash64") | ||
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Member
There was a problem hiding this comment. Do we really need to add an entirely new package dependency to PEcAn just for this one call in one function? Is there an easier solution, or one that relies on existing packages?
Member
There was a problem hiding this comment. Doesn't necessarily warrant using it, but that was my suggestion since I was using it in ccmmf workflows, and it was already a dependency b/c of the api. Line 14 in 7faa280 |
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| return(uid) | ||
| } | ||
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Package added as a dependency, but I can't find any places in your PR where it's actually used. Can this be removed?