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1 #!/usr/bin/env Rscript
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2
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3 suppressPackageStartupMessages(library("data.table"))
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4 suppressPackageStartupMessages(library("optparse"))
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5
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6 option_list <- list(
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7 make_option(c("--input_dir"), action="store", dest="input_dir", help="Directory containing .csv outputs from insect_phenology_model"),
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8 make_option(c("--start_date"), action="store", dest="start_date", default=NULL, help="Start date for custom date interval"),
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9 make_option(c("--script_dir"), action="store", dest="script_dir", help="R script source directory")
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10 )
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11
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12 parser <- OptionParser(usage="%prog [options] file", option_list=option_list);
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13 args <- parse_args(parser, positional_arguments=TRUE);
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14 opt <- args$options;
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15
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16 get_new_temperature_data_frame = function(input_file) {
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17 temperature_data_frame = read.csv(file=input_file, header=T, strip.white=TRUE, stringsAsFactors=FALSE, sep=",");
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18 colnames(temperature_data_frame) = c("LATITUDE", "LONGITUDE", "DATE", "DOY", "TMIN", "TMAX");
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19 return(temperature_data_frame);
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20 }
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21
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22 # Import the shared utility functions.
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23 utils_path <- paste(opt$script_dir, "utils.R", sep="/");
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24 source(utils_path);
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25
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26 # FIXME: currently custom date fields are free text, but
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27 # Galaxy should soon include support for a date selector
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28 # at which point this tool should be enhanced to use it.
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29 # Validate start_date.
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30
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31 # Calaculate the number of days in the date interval.
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32 start_date = validate_date(opt$start_date);
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33 # Validate end_date.
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34 end_date = validate_date(opt$end_date);
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35 if (start_date >= end_date) {
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36 stop_err("The start date must be between 1 and 50 days before the end date when setting date intervals for plots.");
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37 }
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38 # Calculate the number of days in the date interval.
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39 num_days = difftime(end_date, start_date, units=c("days"));
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40 # Add 1 to the number of days to make the dates inclusive. For
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41 # example, if the user enters a date range of 2018-01-01 to
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42 # 2018-01-31, they likely expect the end date to be included.
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43 num_days = num_days + 1;
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44 if (num_days > 50) {
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45 # We need to restrict date intervals since
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46 # plots render tick marks for each day.
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47 stop_err("Date intervals for plotting cannot exceed 50 days.");
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48 }
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49 # Display the total number of days in the Galaxy history item blurb.
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50 cat("Number of days in date interval: ", num_days, "\n");
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51
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52 # Get the year from the start_date.
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53 year = get_year_from_date(start_date);
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54 # Get the DOY for start_date and end_date.
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55 start_date_doy = as.integer(strftime(start_date, format="%j"));
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56 end_date_doy = as.integer(strftime(end_date, format="%j"));
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57 # Get the ticks date labels for plots.
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58 ticks_and_labels = get_x_axis_ticks_and_labels(temperature_data_frame, prepend_end_doy_norm, append_start_doy_norm, date_interval=TRUE);
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59 ticks = c(unlist(ticks_and_labels[1]));
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60 date_labels = c(unlist(ticks_and_labels[2]));
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61 # All latitude values are the same, so get the value
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62 # for plots from the first row.
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63 latitude = temperature_data_frame$LATITUDE[1];
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64
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65 input_files = list.files(path=input_dir, full.names=TRUE);
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66 for(input_file in input_files) {
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67 temperature_data_frame = get_new_temperature_data_frame(input_file);
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68 start_date_row = which(temperature_data_frame$DATE==start_date);
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69 end_date_row = which(temperature_data_frame$DATE==end_date);
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70 # Extract the date interval.
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71 temperature_data_frame = temperature_data_frame[start_date_row:end_date_row,];
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72 # Save the date interval data into an output file
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73 # named the same as the input.
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74 file_path = paste("output_data_dir", input_file, sep="/");
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75 write.csv(temperature_data_frame, file=file_path, row.names=F);
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76 # TODO: Save the dat interval plots...
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77 }
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