wip: starting from_tsv implementation

annotation · Mar 27, 2023 · 2071936 · 2071936
1 parent c25899d
commit 2071936
Show file tree

Hide file tree

Showing 2 changed files with 70 additions and 5 deletions.
diff --git a/src/bin/stam/main.rs b/src/bin/stam/main.rs
@@ -6,14 +6,14 @@ mod annotate;
 mod info;
 mod tag;
 mod to_text;
-mod to_tsv;
+mod tsv;
 mod validate;
 
 use crate::annotate::*;
 use crate::info::*;
 use crate::tag::*;
 use crate::to_text::*;
-use crate::to_tsv::*;
+use crate::tsv::*;
 use crate::validate::*;
 
 const VERSION: &'static str = env!("CARGO_PKG_VERSION");

diff --git a/src/bin/stam/to_tsv.rs → src/bin/stam/tsv.rs b/src/bin/stam/to_tsv.rs → src/bin/stam/tsv.rs
@@ -4,6 +4,8 @@ use stam::{
     Storable, TextResource, TextResourceHandle, TextSelection,
 };
 use std::fmt;
+use std::fs::File;
+use std::io::{BufRead, BufReader};
 use std::process::exit;
 
 pub fn tsv_arguments<'a>() -> Vec<clap::Arg<'a>> {
@@ -500,9 +502,9 @@ impl Column {
     }
 }
 
-struct ColumnConfig(Vec<Column>);
+struct Columns(Vec<Column>);
 
-impl ColumnConfig {
+impl Columns {
     fn printrow(
         &self,
         store: &AnnotationStore,
@@ -540,7 +542,7 @@ pub fn to_tsv(
     null: &str,
     header: bool,
 ) {
-    let columns = ColumnConfig(
+    let columns = Columns(
         columnconfig
             .iter()
             .map(|col| {
@@ -689,3 +691,66 @@ pub fn to_tsv(
         }
     }
 }
+
+pub fn from_tsv(
+    store: &mut AnnotationStore,
+    filename: &str,
+    columns: Vec<&str>,
+    tp: Option<Type>,
+    flattened: bool,
+    delimiter: &str,
+    null: &str,
+    has_header: bool,
+) {
+    let f = File::open(filename).unwrap_or_else(|e| {
+        eprintln!("Error opening rules {}: {}", filename, e);
+        exit(1)
+    });
+    let reader = BufReader::new(f);
+
+    let mut columns = Columns(
+        columns
+            .iter()
+            .map(|col| {
+                Column::try_from(*col)
+                    .map_err(|err| {
+                        eprintln!("{}", err);
+                        exit(1);
+                    })
+                    .unwrap()
+            })
+            .collect(),
+    );
+
+    for (i, line) in reader.lines().enumerate() {
+        if let Ok(line) = line {
+            if line.is_empty() {
+                continue;
+            } else if i == 0 && (has_header || line.starts_with('#')) {
+                //assume a first line with a comment is a header
+                let headerline = if line.starts_with('#') {
+                    line[1..].to_string()
+                } else {
+                    line
+                };
+                columns = Columns(
+                    headerline
+                        .split("\t")
+                        .map(|col| {
+                            Column::try_from(col)
+                                .map_err(|err| {
+                                    eprintln!("{}", err);
+                                    exit(1);
+                                })
+                                .unwrap()
+                        })
+                        .collect(),
+                );
+                continue;
+            } else if line.starts_with('#') {
+                continue;
+            }
+            //TODO
+        }
+    }
+}