patchwork_csv_utils 0.1.22-arm64-darwin → 0.1.24-arm64-darwin
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/Cargo.lock +238 -278
- data/Gemfile +1 -1
- data/Gemfile.lock +5 -3
- data/ext/csv_utils/Cargo.toml +5 -4
- data/ext/csv_utils/src/lib.rs +5 -5
- data/ext/csv_utils/src/utils/csv.rs +160 -167
- data/ext/csv_utils/src/utils/dedup.rs +102 -67
- data/ext/csv_utils/src/utils/mod.rs +81 -17
- data/ext/csv_utils/src/utils/shared/datetime.rs +79 -0
- data/ext/csv_utils/src/utils/shared/filters.rs +130 -0
- data/ext/csv_utils/src/utils/shared/mod.rs +4 -0
- data/ext/csv_utils/src/utils/shared/types.rs +97 -0
- data/ext/csv_utils/src/utils/shared/validation.rs +34 -0
- data/ext/csv_utils/src/utils/xls.rs +272 -184
- data/lib/csv_utils/2.7/csv_utils.bundle +0 -0
- data/lib/csv_utils/3.0/csv_utils.bundle +0 -0
- data/lib/csv_utils/3.1/csv_utils.bundle +0 -0
- data/lib/csv_utils/3.2/csv_utils.bundle +0 -0
- data/lib/csv_utils/version.rb +1 -1
- metadata +8 -3
data/Gemfile
CHANGED
data/Gemfile.lock
CHANGED
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@@ -1,7 +1,7 @@
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PATH
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remote: .
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specs:
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-
patchwork_csv_utils (0.1.
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patchwork_csv_utils (0.1.24)
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GEM
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remote: https://rubygems.org/
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rake (13.2.1)
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rake-compiler (1.2.7)
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rake
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rake-compiler-dock (1.9.1)
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rb_sys (0.9.117)
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rake-compiler-dock (= 1.9.1)
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regexp_parser (2.9.2)
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rexml (3.3.2)
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strscan
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@@ -63,7 +65,7 @@ DEPENDENCIES
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patchwork_csv_utils!
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rake (~> 13.0)
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rake-compiler
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rb_sys (~> 0.9.
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rb_sys (~> 0.9.117)
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rspec (~> 3.0)
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rubocop (~> 1.21)
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data/ext/csv_utils/Cargo.toml
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name = "csv_utils"
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version = "0.1.0"
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edition = "2021"
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rust-version = "1.83"
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authors = ["kingsley.hendrickse <kingsley.hendrickse@patchwork.health>"]
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publish = false
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crate-type = ["cdylib"]
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[dependencies]
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magnus = { version = "0.
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csv = "1.
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calamine = {
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chrono = "0.4
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magnus = { version = "0.8" }
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csv = "1.4"
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calamine = { version = "0.31", features = ["dates"] }
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chrono = "0.4"
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data/ext/csv_utils/src/lib.rs
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use magnus::{define_module, function, prelude::*};
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use crate::utils::csv::transform_csv;
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use crate::utils::dedup::dedup;
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use crate::utils::xls::to_csv;
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use magnus::{function, prelude::*, Ruby};
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pub mod utils;
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#[magnus::init]
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fn init() -> Result<(), magnus::Error> {
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let module = define_module("CsvUtils")?;
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fn init(ruby: &Ruby) -> Result<(), magnus::Error> {
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let module = ruby.define_module("CsvUtils")?;
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module.define_singleton_method("dedup", function!(dedup, 4))?;
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module.define_singleton_method("to_csv", function!(to_csv,
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module.define_singleton_method("transform_csv", function!(transform_csv,
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module.define_singleton_method("to_csv", function!(to_csv, 8))?;
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module.define_singleton_method("transform_csv", function!(transform_csv, 8))?;
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Ok(())
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}
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use chrono::
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use chrono::Utc;
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use csv::{Reader, StringRecord, Writer};
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use magnus::{Error, RArray, Ruby};
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use std::collections::HashMap;
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use std::fs::File;
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use crate::utils::
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use crate::utils::shared::datetime::DateTimeProcessor;
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use crate::utils::shared::filters::RowFilters;
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use crate::utils::shared::types::{HeaderConfig, MandatoryColumn, ProcessingConfig};
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use crate::utils::shared::validation::TrustValidator;
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use crate::utils::{
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check_mandatory_headers, create_header_map, headers_as_byte_record,
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index_of_header_in_mandatory_list, magnus_err, missing_header, missing_value,
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string_to_datetime, FileExtension,
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};
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#[allow(clippy::too_many_arguments)]
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pub fn transform_csv(
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ruby: &Ruby,
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csv_path: String,
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target_path: String,
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exclusions: RArray,
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mandatory_headers: RArray,
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status_exclusions: RArray,
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expected_trust_name: String,
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is_streamed_file: bool,
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earliest_start_date: Option<String>,
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) -> magnus::error::Result<()> {
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if !csv_path.has_extension(&["csv"]) {
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return Err(Error::new(
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return Err(Error::new(
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ruby.exception_standard_error(),
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"csv_path must be a csv file".to_string(),
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));
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}
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let
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let config = ProcessingConfig::from_ruby(
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exclusions,
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mandatory_headers,
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status_exclusions,
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expected_trust_name,
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is_streamed_file,
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earliest_start_date,
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)?;
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let csv_file = File::open(csv_path).map_err(|e| magnus_err(ruby, e, "csv_path"))?;
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let mut csv: Reader<File> = Reader::from_reader(csv_file);
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let mut wtr = Writer::from_path(target_path).map_err(|e| magnus_err(ruby, e, "target_path"))?;
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let headers = csv
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.headers()
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.map_err(|e| magnus_err(ruby, e, "csv_path headers"))?
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.clone();
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let headers_list: Vec<String> = headers.iter().map(|h| h.to_string()).collect();
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if let Some(value) =
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check_mandatory_headers(ruby, &headers_list, &mandatory_headers, "csv")
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check_mandatory_headers(ruby, &headers_list, &config.mandatory_headers, "csv")
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{
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return value;
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}
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let header_map
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let
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let header_map = create_header_map(&config.mandatory_headers);
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let header_config = HeaderConfig::from_header_map(&header_map, ruby)?;
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let inverse_header_map: HashMap<usize, String> = config
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.mandatory_headers
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.iter()
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.enumerate()
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.map(|(i, h)| (i, h.to_string()))
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.collect();
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wtr.write_byte_record(&headers_as_byte_record(config.mandatory_headers.clone()))
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.map_err(|e| magnus_err(ruby, e, "write_byte_record"))?;
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let
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let status = header_map.get("Status");
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let trust_name = header_map.get("Trust").ok_or(missing_header(ruby, "Trust"))?;
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let filters = RowFilters::new(
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config.exclusions,
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config.status_exclusions,
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config.earliest_start_date,
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);
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let trust_validator = TrustValidator::new(config.expected_trust_name, config.is_streamed_file);
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let mandatory_records =
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let mandatory_records =
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get_mandatory_records(ruby, &mut csv, &headers_list, &config.mandatory_headers)?;
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for (ri, record) in mandatory_records.iter().enumerate() {
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if filters.should_skip(
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record,
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header_config.request_id,
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header_config.status,
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header_config.date,
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) {
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continue;
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}
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let mut date_value = Utc::now().naive_utc();
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let columns: Result<Vec<String>, Error> = config
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.mandatory_headers
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.iter()
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.enumerate()
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.map(|(i, column)| {
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let column_index = *header_map
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.get(column)
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.ok_or_else(|| missing_header(ruby, column))?;
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let column_value = record
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.get(column_index)
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.ok_or_else(|| missing_value(ruby, column))?
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.trim_end();
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if i == header_config.trust_name {
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trust_validator.validate(ruby, column_value)?;
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}
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if header_config.is_date_column(i) {
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let current = string_to_datetime(column_value).ok_or_else(|| {
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Error::new(
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ruby.exception_standard_error(),
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format!(
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"Could not parse datetime '{}', row: {}, col: Date",
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column_value, ri
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),
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)
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})?;
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date_value = current;
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Ok(current.to_string())
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} else if header_config.is_time_column(i) {
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if column_value.is_empty() {
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Ok(column_value.to_string())
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} else {
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let column_name = inverse_header_map
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.get(&i)
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.map(|s| s.as_str())
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.unwrap_or("Unknown");
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DateTimeProcessor::new(date_value).process_time_column(
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ruby,
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column_value,
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ri,
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column_name,
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)
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}
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} else {
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let current = process_datetime(ruby, ri, date_value, column_value, &column_name)?;
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columns.push(current);
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Ok(column_value.to_string())
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}
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}
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})
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.collect();
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let record = columns?.into_iter().collect::<StringRecord>();
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wtr.write_byte_record(record.as_byte_record())
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.map_err(|e| magnus_err(ruby, e, "write_byte_record"))?;
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}
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wtr.flush().map_err(|e| magnus_err(ruby, e, "flush"))?;
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@@ -92,110 +152,43 @@ pub fn transform_csv(ruby: &Ruby,
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Ok(())
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}
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}
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let current_time = string_to_time(c).ok_or(to_datetime_error(ruby, c, ri, column_name))?;
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let datetime = transform_time_to_datetime(date_value, current_time);
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Ok(datetime.to_string())
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-
}
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fn get_column_name(inverse_header_map: &HashMap<usize, String>, i: &usize) -> String {
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let unknown = "Unknown".to_string();
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141
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let column_name = inverse_header_map.get(&i).unwrap_or(&unknown);
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column_name.to_string()
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155
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fn get_mandatory_records(
|
|
156
|
+
ruby: &Ruby,
|
|
157
|
+
csv: &mut Reader<File>,
|
|
158
|
+
csv_header_list: &[String],
|
|
159
|
+
mandatory_headers_list: &[String],
|
|
160
|
+
) -> magnus::error::Result<Vec<StringRecord>> {
|
|
161
|
+
let inverse_header_map: HashMap<usize, String> = csv_header_list
|
|
162
|
+
.iter()
|
|
163
|
+
.enumerate()
|
|
164
|
+
.map(|(i, h)| (i, h.to_string()))
|
|
165
|
+
.collect();
|
|
166
|
+
|
|
167
|
+
csv.records()
|
|
168
|
+
.map(|row_result| {
|
|
169
|
+
let row = row_result.map_err(|e| magnus_err(ruby, e, "record error"))?;
|
|
170
|
+
|
|
171
|
+
let mut columns: Vec<MandatoryColumn<String>> = row
|
|
172
|
+
.iter()
|
|
173
|
+
.enumerate()
|
|
174
|
+
.filter_map(|(i, column_value)| {
|
|
175
|
+
inverse_header_map.get(&i).and_then(|column_name| {
|
|
176
|
+
if mandatory_headers_list.contains(column_name) {
|
|
177
|
+
index_of_header_in_mandatory_list(
|
|
178
|
+
mandatory_headers_list.to_vec(),
|
|
179
|
+
column_name.to_string(),
|
|
180
|
+
)
|
|
181
|
+
.map(|index| MandatoryColumn::new(column_value.to_string(), index))
|
|
182
|
+
} else {
|
|
183
|
+
None
|
|
184
|
+
}
|
|
185
|
+
})
|
|
186
|
+
})
|
|
187
|
+
.collect();
|
|
188
|
+
|
|
189
|
+
columns.sort_by_key(|c| c.index);
|
|
190
|
+
|
|
191
|
+
Ok(columns.into_iter().map(|c| c.value).collect())
|
|
192
|
+
})
|
|
193
|
+
.collect()
|
|
143
194
|
}
|
|
144
|
-
|
|
145
|
-
fn skip_excluded_rows(request_id: &usize, status: &Option<&usize>, r: &StringRecord, exclusions: &Vec<String>) -> bool {
|
|
146
|
-
if let Some(status_index) = status {
|
|
147
|
-
if let Some(status) = r.get(**status_index) {
|
|
148
|
-
if status.eq("Recalled") {
|
|
149
|
-
return false
|
|
150
|
-
}
|
|
151
|
-
}
|
|
152
|
-
}
|
|
153
|
-
|
|
154
|
-
let value = r.get(*request_id).unwrap_or_default();
|
|
155
|
-
exclusions.contains(&value.to_string())
|
|
156
|
-
}
|
|
157
|
-
|
|
158
|
-
fn skip_excluded_status_rows(status: &Option<&usize>, r: &StringRecord, exclusions: &Vec<String>) -> bool {
|
|
159
|
-
status
|
|
160
|
-
.map(|index| exclusions.contains(&r[*index].to_string()))
|
|
161
|
-
.unwrap_or(false)
|
|
162
|
-
}
|
|
163
|
-
|
|
164
|
-
fn string_to_datetime(s: &str) -> Option<NaiveDateTime> {
|
|
165
|
-
let maybe_correct = correct_datetime(s);
|
|
166
|
-
if maybe_correct.is_some() { return maybe_correct; }
|
|
167
|
-
|
|
168
|
-
NaiveDate::parse_from_str(s, "%d-%b-%y").ok().map(|d| d.and_hms_opt(0, 0, 0)).flatten()
|
|
169
|
-
}
|
|
170
|
-
|
|
171
|
-
fn correct_datetime(s: &str) -> Option<NaiveDateTime> {
|
|
172
|
-
NaiveDateTime::parse_from_str(s, "%Y-%m-%d %H:%M:%S").ok()
|
|
173
|
-
}
|
|
174
|
-
|
|
175
|
-
fn string_to_time(s: &str) -> Option<NaiveTime> {
|
|
176
|
-
NaiveTime::parse_from_str(s, "%H:%M").ok()
|
|
177
|
-
}
|
|
178
|
-
|
|
179
|
-
fn transform_time_to_datetime(t1: NaiveDateTime, t2: NaiveTime) -> NaiveDateTime {
|
|
180
|
-
NaiveDateTime::new(t1.date(), t2)
|
|
181
|
-
}
|
|
182
|
-
|
|
183
|
-
fn has_empty_first_col_skip_row(record: &StringRecord) -> bool {
|
|
184
|
-
record[0].is_empty()
|
|
185
|
-
}
|
|
186
|
-
|
|
187
|
-
fn has_empty_row_skip(record: &StringRecord) -> bool {
|
|
188
|
-
record.iter().all(|r| r.is_empty())
|
|
189
|
-
}
|
|
190
|
-
|
|
191
|
-
#[derive(Debug, PartialOrd, PartialEq, Eq, Ord)]
|
|
192
|
-
struct CsvMandatoryColumn {
|
|
193
|
-
value: String,
|
|
194
|
-
index: usize,
|
|
195
|
-
}
|
|
196
|
-
|
|
197
|
-
impl CsvMandatoryColumn {
|
|
198
|
-
fn new(value: String, index: usize) -> Self {
|
|
199
|
-
CsvMandatoryColumn { value, index }
|
|
200
|
-
}
|
|
201
|
-
}
|
|
@@ -3,92 +3,127 @@ use std::fs::File;
|
|
|
3
3
|
use csv::{Reader, StringRecord, Writer};
|
|
4
4
|
use magnus::{RArray, Ruby};
|
|
5
5
|
|
|
6
|
-
use crate::utils::
|
|
7
|
-
|
|
8
|
-
|
|
9
|
-
|
|
10
|
-
|
|
11
|
-
|
|
6
|
+
use crate::utils::shared::filters::FilterableRecord;
|
|
7
|
+
use crate::utils::{
|
|
8
|
+
check_mandatory_headers, create_header_map, headers_as_byte_record, magnus_err, missing_header,
|
|
9
|
+
missing_value, FileExtension,
|
|
10
|
+
};
|
|
11
|
+
|
|
12
|
+
pub fn dedup(
|
|
13
|
+
ruby: &Ruby,
|
|
14
|
+
previous_csv_path: String,
|
|
15
|
+
new_csv_path: String,
|
|
16
|
+
target_path: String,
|
|
17
|
+
mandatory_headers: RArray,
|
|
12
18
|
) -> magnus::error::Result<()> {
|
|
13
|
-
|
|
14
|
-
|
|
15
|
-
|
|
16
|
-
if let Some(value) =
|
|
17
|
-
check_file_extension(ruby, &new_csv_path, "new_csv_path") { return value; }
|
|
19
|
+
validate_csv_extension(ruby, &previous_csv_path, "previous_csv_path")?;
|
|
20
|
+
validate_csv_extension(ruby, &new_csv_path, "new_csv_path")?;
|
|
18
21
|
|
|
19
|
-
let csv1 =
|
|
22
|
+
let csv1 =
|
|
23
|
+
File::open(previous_csv_path).map_err(|e| magnus_err(ruby, e, "previous_csv_path"))?;
|
|
20
24
|
let csv2 = File::open(new_csv_path).map_err(|e| magnus_err(ruby, e, "new_csv_path"))?;
|
|
21
25
|
|
|
22
26
|
let mandatory_headers: Vec<String> = RArray::to_vec(mandatory_headers)?;
|
|
23
27
|
|
|
24
|
-
let mut previous_csv:
|
|
25
|
-
let mut new_csv:
|
|
28
|
+
let mut previous_csv: Reader<File> = Reader::from_reader(csv1);
|
|
29
|
+
let mut new_csv: Reader<File> = Reader::from_reader(csv2);
|
|
26
30
|
|
|
27
31
|
let mut wtr = Writer::from_path(target_path).map_err(|e| magnus_err(ruby, e, "target_path"))?;
|
|
28
32
|
|
|
29
|
-
let previous_headers = previous_csv
|
|
30
|
-
|
|
31
|
-
|
|
32
|
-
|
|
33
|
-
|
|
34
|
-
|
|
35
|
-
|
|
36
|
-
|
|
37
|
-
|
|
38
|
-
|
|
39
|
-
|
|
40
|
-
|
|
41
|
-
let
|
|
42
|
-
|
|
43
|
-
|
|
44
|
-
|
|
45
|
-
|
|
33
|
+
let previous_headers = previous_csv
|
|
34
|
+
.headers()
|
|
35
|
+
.map_err(|e| magnus_err(ruby, e, "previous_csv"))?
|
|
36
|
+
.clone();
|
|
37
|
+
let previous_headers_list: Vec<String> =
|
|
38
|
+
previous_headers.iter().map(|h| h.to_string()).collect();
|
|
39
|
+
let new_headers = new_csv
|
|
40
|
+
.headers()
|
|
41
|
+
.map_err(|e| magnus_err(ruby, e, "new_csv"))?
|
|
42
|
+
.clone();
|
|
43
|
+
let new_headers_list: Vec<String> = new_headers.iter().map(|h| h.to_string()).collect();
|
|
44
|
+
|
|
45
|
+
if let Some(err) = check_mandatory_headers(
|
|
46
|
+
ruby,
|
|
47
|
+
&previous_headers_list,
|
|
48
|
+
&mandatory_headers,
|
|
49
|
+
"previous_csv",
|
|
50
|
+
) {
|
|
51
|
+
return err;
|
|
52
|
+
}
|
|
46
53
|
|
|
47
|
-
|
|
48
|
-
|
|
49
|
-
|
|
50
|
-
|
|
54
|
+
if let Some(err) =
|
|
55
|
+
check_mandatory_headers(ruby, &new_headers_list, &mandatory_headers, "new_csv")
|
|
56
|
+
{
|
|
57
|
+
return err;
|
|
51
58
|
}
|
|
52
59
|
|
|
60
|
+
wtr.write_byte_record(&headers_as_byte_record(mandatory_headers.clone()))
|
|
61
|
+
.map_err(|e| magnus_err(ruby, e, "write_byte_record"))?;
|
|
62
|
+
|
|
63
|
+
let previous_records = get_records(
|
|
64
|
+
ruby,
|
|
65
|
+
&mut previous_csv,
|
|
66
|
+
&previous_headers_list,
|
|
67
|
+
&mandatory_headers,
|
|
68
|
+
)?;
|
|
69
|
+
let new_records = get_records(ruby, &mut new_csv, &new_headers_list, &mandatory_headers)?;
|
|
70
|
+
|
|
71
|
+
new_records
|
|
72
|
+
.into_iter()
|
|
73
|
+
.filter(|record| !previous_records.contains(record))
|
|
74
|
+
.try_for_each(|record| {
|
|
75
|
+
wtr.write_byte_record(record.as_byte_record())
|
|
76
|
+
.map_err(|e| magnus_err(ruby, e, "write_byte_record"))
|
|
77
|
+
})?;
|
|
78
|
+
|
|
53
79
|
wtr.flush().map_err(|e| magnus_err(ruby, e, "flush"))?;
|
|
54
80
|
|
|
55
81
|
Ok(())
|
|
56
82
|
}
|
|
57
83
|
|
|
58
|
-
fn get_records(
|
|
59
|
-
|
|
60
|
-
|
|
61
|
-
|
|
62
|
-
|
|
63
|
-
|
|
64
|
-
|
|
65
|
-
|
|
66
|
-
|
|
67
|
-
|
|
68
|
-
|
|
69
|
-
|
|
70
|
-
|
|
71
|
-
|
|
72
|
-
|
|
73
|
-
|
|
74
|
-
|
|
75
|
-
|
|
76
|
-
|
|
84
|
+
fn get_records(
|
|
85
|
+
ruby: &Ruby,
|
|
86
|
+
csv: &mut Reader<File>,
|
|
87
|
+
csv_headers: &[String],
|
|
88
|
+
headers: &[String],
|
|
89
|
+
) -> magnus::error::Result<Vec<StringRecord>> {
|
|
90
|
+
let header_map = create_header_map(csv_headers);
|
|
91
|
+
|
|
92
|
+
csv.records()
|
|
93
|
+
.filter_map(|record_result| match record_result {
|
|
94
|
+
Ok(record) if !record.is_empty() && !record.has_empty_first_column() => {
|
|
95
|
+
Some(Ok(record))
|
|
96
|
+
}
|
|
97
|
+
Ok(_) => None,
|
|
98
|
+
Err(e) => Some(Err(magnus_err(ruby, e, "record error"))),
|
|
99
|
+
})
|
|
100
|
+
.map(|record_result| {
|
|
101
|
+
let record = record_result?;
|
|
102
|
+
|
|
103
|
+
let columns: Result<Vec<&str>, magnus::Error> = headers
|
|
104
|
+
.iter()
|
|
105
|
+
.map(|column| {
|
|
106
|
+
let column_index = *header_map
|
|
107
|
+
.get(column)
|
|
108
|
+
.ok_or_else(|| missing_header(ruby, column))?;
|
|
109
|
+
record
|
|
110
|
+
.get(column_index)
|
|
111
|
+
.map(|s| s.trim_end())
|
|
112
|
+
.ok_or_else(|| missing_value(ruby, column))
|
|
113
|
+
})
|
|
114
|
+
.collect();
|
|
115
|
+
|
|
116
|
+
Ok(columns?.into_iter().collect::<StringRecord>())
|
|
117
|
+
})
|
|
118
|
+
.collect()
|
|
77
119
|
}
|
|
78
120
|
|
|
79
|
-
fn
|
|
121
|
+
fn validate_csv_extension(ruby: &Ruby, csv_path: &str, message: &str) -> magnus::error::Result<()> {
|
|
80
122
|
if !csv_path.has_extension(&["csv"]) {
|
|
81
|
-
return
|
|
123
|
+
return Err(magnus::Error::new(
|
|
124
|
+
ruby.exception_standard_error(),
|
|
125
|
+
format!("{} must be a csv file", message),
|
|
126
|
+
));
|
|
82
127
|
}
|
|
83
|
-
|
|
84
|
-
}
|
|
85
|
-
|
|
86
|
-
fn has_empty_first_col_skip_row(previous_record: &StringRecord) -> bool {
|
|
87
|
-
previous_record[0].is_empty()
|
|
88
|
-
}
|
|
89
|
-
|
|
90
|
-
fn has_empty_row_skip(record: &StringRecord) -> bool {
|
|
91
|
-
record.iter().all(|r| r.is_empty())
|
|
128
|
+
Ok(())
|
|
92
129
|
}
|
|
93
|
-
|
|
94
|
-
|